-
Notifications
You must be signed in to change notification settings - Fork 0
/
ran_script.txt
1000 lines (1000 loc) · 68 KB
/
ran_script.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001 cd ..
1002 head Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
1003 sed -i 's/ /_/g' Arab_thali.fa
1004 head Arab_thali.fa
1005 gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +/ ) {gsub(/ +/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' Arabidopsis_thaliana.TAIR10.fa > Arab_thali.fa
1006 sudo apt install gawt
1007 sudo apt install gawk
1008 gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +/ ) {gsub(/ +/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' Arabidopsis_thaliana.TAIR10.fa > Arab_thali.fa
1009 head Arab_thali.fa
1010 perl -i.bak -pe "s/\s+$/\n/;" Arab_thali.fa
1011 head Arab_thali.fa
1012 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed1.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa 2> wt-ABA-3_report.log
1013 cd Mirdeep_miRNA/
1014 head wt-ABA-3_collapsed1.fa
1015 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa 2> wt-ABA-3_report.log
1016 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa
1017 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none none
1018 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1019 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fasta Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1020 ls
1021 head wt-ABA-3_collapsed.fasta
1022 head wt-ABA-3_collapsed1.fasta
1023 sed -i 's/x/x /g' wt-ABA-3_collapsed1.fasta
1024 head wt-ABA-3_collapsed1.fasta
1025 cd ..
1026 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed1.fastaa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1027 cd ..
1028 cd microRNA_data/
1029 sanity_check_genome.pl Arab_thali.fa
1030 remove_white_space_in_id.pl Arab_thali.fa
1031 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fasta Arab_thali.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1032 head Arab_thali.fa
1033 cd Documents/
1034 cd microRNA_data/
1035 ls -l
1036 cd ..
1037 ls -l
1038 perl -MCPAN -e shell
1039 sudo perl -MCPAN -e shell
1040 curl -L http://xrl.us/installperlnix | bash
1041 exit
1042 perl -v
1043 cpan App::cpanminus
1044 perl -MCPAN -e shell
1045 sudo perl -MCPAN -e shell
1046 sudo apt-get install libterm-readline-gnu-perlsudo apt-get install libterm-readline-gnu-perl
1047 sudo apt-get install libterm-readline-gnu-perl
1048 perl -MCPAN -e shell
1049 sudo perl -MCPAN -e shell
1050 celar
1051 clear
1052 whereis htseq-count
1053 ls
1054 whereis python
1055 whereis mirdeep2
1056 whereis htseq-count
1057 clear
1058 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1059 ls -l
1060 cd mirPRo.1.1.4/
1061 clear
1062 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1063 cd ..
1064 ls -l
1065 cd mirdeep2/
1066 clear
1067 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa 2> wt-ABA-3_report.log
1068 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa
1069 clear
1070 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1071 Error: Perl PDF::API2 package not found
1072 sudo cpan PDF::API2
1073 make_html.pl
1074 clear
1075 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1076 clear
1077 cd mirdeep2/
1078 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1079 cd ..
1080 clear
1081 ls -l
1082 cd mirPRo.1.1.4/
1083 clear
1084 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1085 samtools -version
1086 cd ..
1087 ls -l
1088 cd samtools-1.9/
1089 ls -l
1090 make
1091 pwd
1092 /home/siva/samtools-1.9
1093 export PATH=$PATH: /home/siva/samtools-1.9
1094 cd ..
1095 cd mirPRo.1.1.4/
1096 ls
1097 clear
1098 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1099 clear
1100 cd ..
1101 ls
1102 ls -l
1103 clear
1104 git clone https://github.com/jehandzlik/Manatee.git
1105 cd Manatee/
1106 ls -l
1107 ./config
1108 sudo ./config
1109 cpan
1110 sudo cpan
1111 Manatee -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
1112 ls -l
1113 clear
1114 manatee -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
1115 cd ..
1116 mkdir samtools
1117 ls -l
1118 cd samtools
1119 make
1120 cd ..
1121 cd samtools-1.9/
1122 make
1123 make install
1124 sudo make install
1125 cd ..
1126 cd Manatee/
1127 clear
1128 manatee -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
1129 nano manatee
1130 pwd
1131 cpan App::cpanminus
1132 sudo cpan App::cpanminus
1133 ls -l
1134 chmod 755 unitas/
1135 cd unitas/
1136 clear
1137 ls -l
1138 unitas_1.7.0.pl -h
1139 perl unitas_1.7.0.pl
1140 cpan
1141 clear
1142 perl unitas_1.7.0.pl
1143 perl -v
1144 perl unitas_1.7.0.pl
1145 cpan
1146 sudo cpan
1147 perl unitas_1.7.0.pl
1148 sudo cpan
1149 perl unitas_1.7.0.pl
1150 ls -l
1151 cd mirdeep2/
1152 ls
1153 clear
1154 ls -l
1155 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
1156 Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa
1157 cd ..
1158 cd Documents/
1159 clear
1160 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa \
1161 Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
1162 Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf \
1163 cd microRNA_data/
1164 clear
1165 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa \
1166 Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
1167 Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf \
1168 clear
1169 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1170 cd ..
1171 cd mirdeep2/
1172 ls
1173 perl install.pl
1174 install.pl
1175 perl install.pl
1176 cd ..
1177 cd Documents/microRNA_data/
1178 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1179 cd Documents/microRNA_data/
1180 clear
1181 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1182 cd ..
1183 tar xvvzf PDF-API2-0.73.tar.gz
1184 cd PDF-API2-0.73/
1185 whereis miRDeep2
1186 perl Makefile.PL INSTALL_BASE= /home/siva/mirdeep2/bin/miRDeep2.pl LIB= /home/siva/mirdeep2/bin/miRDeep2.pl/lib
1187 perl Makefile.PL INSTALL_BASE= /home/siva/mirdeep2/bin/miRDeep2.pl LIB= /home/siva/mirdeep2/lib
1188 perl Makefile.PL INSTALL_BASE= /home/siva/mirdeep2/ LIB= /home/siva/mirdeep2/lib
1189 cd ..
1190 cd PDF-API2-0.73/
1191 echo $PATH
1192 cd ..
1193 git clone https://github.com/BenLangmead/bowtie.git
1194 cd bowtie/
1195 echo $PATH
1196 bowtie -version
1197 whereis bowtie
1198 whereis mirdeep2
1199 cd ..
1200 whereis mirdeep2
1201 cd mirdeep2/
1202 echo $PATH
1203 echo $PATH &>PATH
1204 cd ..
1205 whereis Vienna
1206 cd ViennaRNA-2.4.16/
1207 echo $PATH
1208 pwd
1209 ls
1210 cd ..
1211 cd randfold_src/
1212 pwd
1213 cd ..
1214 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1215 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1216 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1217 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1218 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1219 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1220 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1221 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1222 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1223 echo '/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1224 echo '/home/siva/randfold_src' >> ~/.bashrc
1225 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1226 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1227 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1228 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1229 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1230 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1231 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1232 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1233 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1234 echo '/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1235 echo '/home/siva/randfold_src' >> ~/.bashrc
1236 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1237 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1238 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1239 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1240 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1241 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1242 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1243 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1244 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1245 echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1246 echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
1247 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1248 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1249 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1250 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1251 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1252 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1253 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1254 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1255 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1256 echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1257 echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
1258 bowtie
1259 RNAfold -h
1260 randfold
1261 make_html
1262 make_html.pl
1263 clear
1264 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1265 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1266 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1267 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1268 echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1269 echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
1270 cd mirdeep2/
1271 cd ..
1272 cd Documents/microRNA_data/
1273 ls -l
1274 clear
1275 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1276 cd ..
1277 cd..
1278 cd ..
1279 cd bowtie/
1280 pwd
1281 echo 'export PATH=$PATH:/home/siva/bowtie' >> ~/.bashrc
1282 clear
1283 cd Documents/microRNA_data/
1284 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1285 cd Documents/microRNA_data/
1286 clear
1287 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1288 whereis bowtie
1289 locate bowtie
1290 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1291 echo 'export PATH=$PATH:/home/siva/bowtie' >> ~/.bashrc
1292 exit
1293 cd Documents/microRNA_data/
1294 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1295 cd ..
1296 cd ViennaRNA-2.4.16/
1297 ls -l
1298 ./configure
1299 make
1300 clear
1301 pwd
1302 ls -l
1303 python -version
1304 python --version
1305 where is Python
1306 whereis Python
1307 $PATH Python
1308 nano bash.src
1309 nano bashrc.sh
1310 $PATH
1311 pwd
1312 ls -l
1313 conda install -c conda-forge mamba
1314 clear
1315 mamba create -c conda-forge -c bioconda -n snakemake snakemake
1316 conda activate snakemake
1317 snakemake --help
1318 snakemake --version
1319 exit
1320 clear
1321 cd Documents/microRNA_data/
1322 clear
1323 mapper.pl TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m /
1324 -p bowtie_index/arabidopsis_genome /
1325 -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa /
1326 -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf /
1327 -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1328 cd Mirdeep_miRNA/
1329 find_read_count.pl wt-ABA-3_collapsed.fasta
1330 cd ..
1331 whereis bowtie-build
1332 whereis mirdeep2
1333 cd ..
1334 cd mirdeep2/
1335 cd ..
1336 cd Documents/microRNA_data/
1337 clear
1338 mapper.pl TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1339 mapper.pl TRIMMED/wt-ABA-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-1_collapsed.fa -t Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-1.txt
1340 mapper.pl TRIMMED/wt-ABA-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-2_collapsed.fa -t Mirdeep_miRNA/wt-ABA-2_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-2.txt
1341 mapper.pl TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1342 mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-Control-1.txt
1343 mapper.pl TRIMMED/wt-Control-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-2_collapsed.fa -t Mirdeep_miRNA/wt-Control-2_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-Control-2.txt
1344 mapper.pl TRIMMED/wt-Control-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-3_collapsed.fa -t Mirdeep_miRNA/wt-Control-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-Control-3.txt
1345 clear
1346 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-ABA-1_collapsed.fa -y now -d
1347 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-ABA-2_collapsed.fa -y now -d
1348 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-ABA-3_collapsed.fa -y now -d
1349 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-1_collapsed.fa -y now -d
1350 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-2_collapsed.fa -y now -d
1351 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-3_collapsed.fa -y now -d
1352 whereis samtools
1353 whereis bowtie
1354 clear
1355 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1356 cpan install PDF::API2
1357 sudo cpan install PDF::API2
1358 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1359 perldoc PDF::API2
1360 cd ..
1361 cd PDF-API2-0.73/
1362 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1363 cd ..
1364 conda install -c bioconda perl-pdf-api2
1365 perldoc PDF::API2
1366 whereis PDF::API2
1367 locate PDF::API2
1368 nano bashrc.sh
1369 nano .bashrc
1370 cd Documents/microRNA_data/
1371 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1372 cd ...
1373 cd ..
1374 tar xvvzf PDF-API2-0.73.tar.gz
1375 cd PDF-API2-0.73/
1376 pwd
1377 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1378 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/ LIB=/home/siva/mirdeep2/lib/
1379 perl Makefile.PL INSTALL_BASE=/home/siva/ LIB=/home/siva/mirdeep2/lib/
1380 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/ LIB=/home/siva/mirdeep2/lib/
1381 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1382 perl -l Makefile.PL INSTALL_BASE=/home/siva/ LIB=/home/siva/mirdeep2/lib
1383 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/essentials/PDF-API2-XS-1.001 PREFIX=/home/siva/mirdeep2/lib LIB=/home/siva/mirdeep2/lib
1384 cd ..
1385 cd mirdeep2/
1386 cd /home/siva/mirdeep2/essentials/PDF-API2-XS-1.001
1387 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/essentials/PDF-API2-XS-1.001 PREFIX=/home/siva/mirdeep2/lib LIB=/home/siva/mirdeep2/lib
1388 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/essentials/PDF-API2-XS-1.001 LIB=/home/siva/mirdeep2/lib
1389 make
1390 make test
1391 make install
1392 cd ..
1393 touch install_successful
1394 nano bashrc
1395 nano bashrc.h
1396 ls -l
1397 nano .bashrc
1398 clear
1399 cd /home/siva/Documents/microRNA_data
1400 bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa ara_gen
1401 sudo apt install bowtie
1402 bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa ara_gen
1403 cd Documents/microRNA_data/
1404 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1405 cd /home/siva/mirdeep2
1406 perl install.pl
1407 cd ..
1408 perl -MCPAN -e 'install Bundle::Compress::Zlib'
1409 cd mirdeep2/
1410 perl install.pl
1411 cd ..
1412 conda install -c bioconda perl-memoize
1413 cd mirdeep2/
1414 perl install.pl
1415 cd ..
1416 % cpanm CHI::Memoize
1417 perl
1418 sudo cpan CHI::Memoize
1419 sudo cpan Bundle::Compress::Zlib
1420 cd mirdeep2/
1421 perl install.pl
1422 nano .bashrc
1423 cd ..
1424 nano .bashrc
1425 cd Documents/microRNA_data/
1426 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1427 cd Documents/microRNA_data/
1428 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1429 cd /home/siva/PDF-API2-0.73
1430 ls -l
1431 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1432 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1433 sudo perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1434 sudo perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/lib/perl5/x86_64-linux/perl5/x86_64-linux/PDF/API2 LIB=/home/siva/mirdeep2/lib
1435 locate Version.pm
1436 cd ..
1437 cd Documents/microRNA_data/
1438 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf -d none none none 2> wt-ABA-1_report.log
1439 cd mirPRo.1.1.4/
1440 fastq_quality_filter -h
1441 fastx_collapser -h
1442 novoindex
1443 novoalign
1444 randfold
1445 RNAfold -h
1446 htseq-count
1447 whereis htseq-count
1448 gcc -v
1449 g++ -v
1450 clear
1451 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1452 htseq-count
1453 samtools
1454 clear
1455 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1456 cd ..
1457 sudo apt-get install python-matplotlib
1458 python
1459 nano .bashrc
1460 cd mirPRo.1.1.4/
1461 bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
1462 bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.bam -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
1463 bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.sorted.out.bam -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
1464 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1465 cd mirdeep2/
1466 perl install.pl
1467 sudo cpan install PDF::API2
1468 perl -MCPAN -e shell
1469 git clone
1470 git clone https://github.com/rajewsky-lab/mirdeep2.git
1471 cd mirdeep2/
1472 perl install.pl
1473 cd ..
1474 cd Documents/microRNA_data/
1475 mapper.pl /TRIMMED/wt-ABA-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1476 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1477 cd Documents/microRNA_data/
1478 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1479 cd ..
1480 cd mirdeep2/
1481 perl install.pl
1482 cd Documents/microRNA_data/
1483 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1484 cd Documents/microRNA_data/
1485 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1486 cd ..
1487 cd mirdeep2/
1488 perl install.pl
1489 exit
1490 cd Documents/microRNA_data/
1491 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1492 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -d -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1493 mapper.pl TRIMMED/wt-Control-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-2_collapsed.fa -t Mirdeep_miRNA/wt-Control-2_collapsed_vs_genome.arf -v
1494 mapper.pl TRIMMED/wt-ABA-3.fastq -e -d -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1495 mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v
1496 mapper.pl TRIMMED/wt-Control-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-2_collapsed.fa -t Mirdeep_miRNA/wt-Control-2_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-2.txt
1497 mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-1.txt
1498 mapper.pl TRIMMED/wt-Control-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-3_collapsed.fa -t Mirdeep_miRNA/wt-Control-3_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-3.txt
1499 mkdir Raw_microRNA_fastq_files
1500 mv *.fastq ./Raw_microRNA_fastq_files/
1501 ls -l
1502 bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa arabidopsis_genome
1503 mv *.ebwt /index
1504 mkdir index
1505 mv *.ebwt /index
1506 mv *.ebwt /index/
1507 ls -l
1508 mv *.ebwt index
1509 ls -l
1510 mkdir micro_RNA
1511 mv * micro_RNA/
1512 cp * micro_RNA/
1513 cp -r * micro_RNA/
1514 cd micr
1515 cd micro_RNA/
1516 ls -l
1517 rm -r micro_RNA/
1518 ls -l
1519 cd ..
1520 gunzip EMBOSS-6.6.0.tar.gz
1521 tar xvf EMBOSS-6.6.0.tar
1522 cd EMBOSS-6.6.0/
1523 ./configure
1524 make
1525 ~~exit
1526 exit
1527 cd Documents/microRNA_data/
1528 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-3 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-3 &
1529 cd Documents/microRNA_data/
1530 pwd
1531 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-3 &
1532 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-3 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-3 &
1533 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1534 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-3 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-3 &
1535 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-3 &
1536 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-2 --bowtie_cores 2 --readfile TRIMMED/wt-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-2 &
1537 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-1 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-1 &
1538 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-3 --bowtie_cores 2 --readfile TRIMMED/wt-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-3 &
1539 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-1 &
1540 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-2 &
1541 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-1 &
1542 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-1 &
1543 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-2 &
1544 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-3 &
1545 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-2 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-2 &
1546 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-2 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-2 &
1547 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-1 --bowtie_cores 2 --readfile TRIMMED/wt-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-1 &
1548 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-2 &
1549 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-2 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-2 &
1550 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-1 &
1551 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-3 &
1552 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-1 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-1 &
1553 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-3 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-3 &
1554 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-2 &
1555 ls -l
1556 cd Documents/
1557 ls -l
1558 cd microRNA_data/
1559 ls -l
1560 cd ShortStack-Results/
1561 ls -l
1562 nano log_wt-ABA-3
1563 nano log_wt-ABA-2
1564 nano log_wt-ABA-1
1565 nano log_wt-Control-1
1566 nano log_wt-Control-3
1567 cd wt-Control-1
1568 ls -l
1569 nano Counts.txt
1570 nano ErrorLogs.txt
1571 nano Results.txt
1572 nano Unplaced.txt
1573 cd MIRNAs/
1574 ls -l
1575 cd ..
1576 rm -all
1577 rm -r *
1578 cd .local/share/Trash/
1579 rm -rf ~/.local/share/Trash/*
1580 cd ~/.local
1581 cd share/
1582 ls -l
1583 cd Trash/
1584 ls -l
1585 cd expunged/
1586 ls -l
1587 cd 475349224/
1588 ls -l
1589 cd Lib/
1590 ls -l
1591 cd ./
1592 cd /
1593 ls
1594 cd /home/siva/Documents/microRNA_data
1595 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-3 &
1596 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-3 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-3 &
1597 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1598 ohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1599 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1600 bin/miRDeep2.pl Mirdeep_results/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_results/wt-ABA-3_collapsed_vs_genome.arf none none none -d 2> Mirdeep_results/wt-ABA-3_report.log
1601 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1602 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-3 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-3 &
1603 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-3 &
1604 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-2 --bowtie_cores 2 --readfile TRIMMED/wt-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-2 &
1605 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-1 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-1 &
1606 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-3 --bowtie_cores 2 --readfile TRIMMED/wt-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-3 &
1607 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-1 &
1608 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-2 &
1609 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-1 &
1610 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-1 &
1611 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-2 &
1612 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-3 &
1613 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-2 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-2 &
1614 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-2 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-2 &
1615 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-1 --bowtie_cores 2 --readfile TRIMMED/wt-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-1 &
1616 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-2 &
1617 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-2 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-2 &
1618 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-1 &
1619 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-3 &
1620 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-1 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-1 &
1621 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-3 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-3 &
1622 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-2 &
1623 do-release upgrade
1624 sudo do-release-upgrade -d
1625 sudo apt-get install
1626 sudo apt-get upgrade
1627 sudo do-release-upgrade -d
1628 sudo apt-get upgrade
1629 sudo do-release-upgrade -d
1630 xkill
1631 sudo shutdown -r now
1632 python get_candidates.py
1633 python2.7 get_candidates.py
1634 python --version
1635 python2
1636 cd ..
1637 python2 get_candidates.py
1638 python --version
1639 which python
1640 sudo apt install python2
1641 python2 --version
1642 python2.7 get_candidates.py
1643 python2.7.17 get_candidates.py
1644 python2 get_candidates.py
1645 python3 --version
1646 python -V
1647 python -v
1648 update-alternatives --list python
1649 sudo update-alternatives --list python
1650 python2.7 get_candidates.py
1651 apt-get install bedtools
1652 sudo apt-get install bedtools
1653 sort -k1,1 -k2,2n miRNA_candidates_v2.bed > candidates.sorted_v2.bed
1654 bedtools merge -i candidates.sorted_v2.bed -d -1 -s -nms > overlapping_v2.txt
1655 pwd
1656 cd Documents/microRNA_data/
1657 python filter.py
1658 python get_fasta.py
1659 python2 get_fasta.py
1660 python format_candidates.py
1661 python2 format_candidates.py
1662 python mature.py
1663 python -V
1664 python mirna_expression.py
1665 python2 mirna_expression.py
1666 python mirna_annotation.py
1667 python2 mirna_expression.py
1668 python mirna_annotation.py
1669 ls
1670 cd mirdeep2/
1671 ls
1672 exit
1673 htseq-count
1674 sudo apt-get remove python-htseq
1675 fastq_quality_filter -h
1676 fastx_collapser -h
1677 novoindex
1678 novoalign
1679 randfold
1680 RNAfold -h
1681 htseq-count
1682 pip install HTSeq==0.6.1
1683 wget https://files.pythonhosted.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz
1684 tar xvvzf HTSeq-0.6.1p1.tar.gz
1685 numpy
1686 novoindex
1687 novoalign
1688 cd mirPRo.1.1.4/
1689 ls
1690 cd ..
1691 cd novocraft/
1692 ls
1693 cd ..
1694 pip install numpy
1695 pip install --upgrade pip
1696 sudo pip install --upgrade pip
1697 pip install pysam
1698 pysam
1699 pySam
1700 conda config --add channels r
1701 conda config --add channels bioconda
1702 conda install pysam
1703 conda install numpy
1704 cd HTSeq-0.6.1p1/
1705 python setup.py build
1706 ls
1707 python2 setup.py build
1708 python setup.py install
1709 python2 setup.py install
1710 sudo python2 setup.py install
1711 cd ..
1712 htseq-count
1713 novoindex
1714 RNAfold -h
1715 htseq-count
1716 gcc -v
1717 g++ -v
1718 ls
1719 rm HTSeq-0.6.1p1.tar.gz
1720 cd mirPRo.1.1.4/
1721 pwd
1722 cd bin/
1723 pwd
1724 /home/siva/mirPRo.1.1.4/bin
1725 export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin
1726 /home/siva/mirPRo.1.1.4/bin
1727 cd ..
1728 cd Documents/microRNA_data/
1729 ls
1730 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1731 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1732 pip install pysam
1733 python3 -m venv env
1734 source ./env/bin/activate
1735 pip install pysam
1736 python3 -m venv env
1737 exit
1738 cd /home/siva/Documents/microRNA_data
1739 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1740 pip install numpy
1741 cd ..
1742 cd HTSeq-0.6.1p1/
1743 python setup.py build/
1744 python2 setup.py build/
1745 python2 setup.py build
1746 python2 setup.py install
1747 python setup.py build
1748 sudo python2 setup.py build
1749 sudo python2 setup.py install
1750 cd ..
1751 cd Documents/microRNA_data/
1752 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1753 samtools
1754 conda install -c bioconda htseq
1755 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1756 conda install samtools=1.9 -y
1757 samtools
1758 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1759 sudo apt-get remove python-htseq
1760 sudo apt autoremove python-htseq
1761 htseq-count
1762 sudo apt autoremove python-htseq
1763 htseq
1764 samtools
1765 sudo apt autoremove htseq
1766 sudo apt-get autoremove --purge python-htseq
1767 sudo apt-get autoremove python-htseq
1768 htseq-count
1769 htseq -h
1770 htseq-count -h
1771 htseq-count --version
1772 locate htseq-count
1773 conda remove htseq-count
1774 rm -rf ~/anaconda3
1775 locate htseq-count
1776 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1777 cd ..
1778 cd mirdeep2/
1779 perl install
1780 perl install.pl
1781 exit
1782 cd Documents/
1783 ls
1784 cd microRNA_data/
1785 ls
1786 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1787 randfold
1788 sudo apt-add-repository ppa:j-4/vienna-rna
1789 sudo apt-get install vienna-rna
1790 cd ..
1791 cd squid-1.9g/
1792 ./configure
1793 make
1794 make check
1795 make install
1796 sudo make
1797 sudo make install
1798 make
1799 cd ..
1800 ls
1801 tar xzvf randfold-2.0.tar.gz
1802 cd randfold-2.0/
1803 make
1804 apt-get install pkg_resources
1805 apt-get install python-setuptools
1806 sudo apt update && apt upgrade
1807 exit
1808 cp randfold /usr/local/bin
1809 exit
1810 cd ViennaRNA-2.4.16/
1811 ./configure
1812 make
1813 randfold
1814 locate htseq-count
1815 pip install pysam
1816 sudo apt-get install gcc
1817 sudo apt-get install make
1818 sudo apt-get update
1819 sudo pip install pysam
1820 cd ..
1821 cd Documents/microRNA_data/
1822 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1823 ls /usr/bin/python*
1824 sudo apt-get remove python3
1825 ls /usr/bin/python*
1826 apt --fix-broken install
1827 sudo apt --fix-broken install
1828 sudo apt autoremove python3
1829 ls /usr/bin/python*
1830 sudo apt install gnome
1831 ls /usr/bin/python*
1832 sudo apt autoremove python
1833 ls /usr/bin/python*
1834 sudo apt-get autoremove python
1835 python --version
1836 python -V
1837 sudo apt-get update
1838 cd /
1839 wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-ppc64le.sh
1840 sudo
1841 cat /etc/os-release
1842 sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
1843 sha256sum /path/filename
1844 Get-FileHash filename -Algorithm SHA256
1845 ls
1846 cd home/
1847 ls
1848 cd siva/
1849 ls
1850 cd ..
1851 pwd
1852 cd siva/
1853 ls
1854 gzip PsFCIV_2.5.zip
1855 gunzip PsFCIV_2.5.zip.gz
1856 sha256sum PsFCIV_2.5.ps1
1857 ls
1858 bash Anaconda3-2020.11-Linux-ppc64le.sh
1859 ls
1860 bash Miniconda2-latest-Linux-x86_64.sh
1861 conda update conda
1862 conda init fish
1863 conda list
1864 pwd
1865 cd miniconda2/
1866 cd bin/
1867 pwd
1868 /home/siva/miniconda2/bin
1869 export PATH=/home/siva/miniconda2/bin
1870 export PATH=/home/siva/miniconda2/bin:$PATH
1871 conda
1872 conda list
1873 conda init fish
1874 conda update conda
1875 conda install pysam
1876 cd ..
1877 ls /usr/bin/python*
1878 pwd
1879 ls
1880 sudo apt-get update
1881 export PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
1882 ls
1883 sudo apt-get update
1884 ls /usr/bin/python*
1885 alias python='/usr/bin/python2.7
1886 . ~/.bashrc
1887 exot
1888 exit
1889 ls /usr/bin/python*
1890 python --versoin
1891 python --version
1892 update-alternatives --list python
1893 sudo apt-add-repository ppa:j-4/vienna-rna
1894 fastq_quality_filter -h
1895 fastx_collapser -h
1896 novoindex
1897 cd novocraft/
1898 ls
1899 pwd
1900 /home/siva/novocraft
1901 export PATH=$PATH:/home/siva/novocraft
1902 novoindex
1903 novoalign
1904 randfold
1905 locate randfold
1906 pwd
1907 cd ..
1908 RNAfold -h
1909 htseq-count
1910 pip install HTSeq==0.6.1p1
1911 sudo pip install HTSeq==0.6.1p1
1912 htseq-count
1913 sudo apt-get install pkg_resources
1914 pip install setuptools
1915 sudo apt-get install pkg_resources
1916 apt-get install python-setuptools
1917 sudo
1918 sudo -s
1919 sudo pip install HTSeq==0.6.1p1
1920 htseq-count
1921 RNAfold -h
1922 randfold
1923 cd randfold-2.0/
1924 make
1925 cd ..
1926 cd randfold_src/
1927 cd src/
1928 make
1929 randfold
1930 path
1931 touch PATH
1932 $PATH
1933 cp randfold /usr/local/bin
1934 sudo -s
1935 randfold
1936 ls
1937 rm randfold-2.0.tar.gz
1938 rm randfold-2.0
1939 rm -r randfold-2.0
1940 ls
1941 randfold
1942 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1943 pwd
1944 mv -r mirPro_results/ /home/siva/Documents/microRNA_data
1945 mv mirPro_results/ /home/siva/Documents/microRNA_data
1946 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> /mirPro_results/wt-Control-1.txt
1947 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirPro_results/wt-Control-1.txt
1948 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> ./mirPro_results/wt-Control-1.txt
1949 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> ./mirPro_results/wt_Control_1.txt
1950 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirpro_wt_Control_1.txt
1951 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirpro_wt_Control_2.txt
1952 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirpro_wt_Control_3.txt
1953 cd Documents/microRNA_data/
1954 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq
1955 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1956 sudo qpt-get update
1957 sudo nano /etc/NetworkManager/NetworkManager.conf
1958 sudo service network-manager restart
1959 sudo touch /etc/NetworkManager/conf.d/10-globally-managed-devices.conf
1960 sudo systemct1 restart NetworkManager
1961 sudo dhclient
1962 sudo apt-get update
1963 sudo apt-get upgrade
1964 sudo snap install notepad-plus-plus
1965 sudo apt-get upgrade
1966 sudo apt-get update
1967 nohup /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1968* nohup /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx >mirpro_scipt.txt 2>ran_scrip.txt
1969 history >hist.txt
1970 pwd
1971 cd Documents/Webinar/
1972 mv * /home/siva/Documents/
1973 cd ..
1974 rmdr Webinar/
1975 rm Webinar/
1976 rm -r Webinar/
1977 cd microRNA_data/
1978 ls
1979 scp -r fastX_toolkit_STATUS/ [email protected]:/microRNA_sequencing
1980 scp -r fastX_toolkit_STATUS/ [email protected]
1981 sftp -r fastX_toolkit_STATUS/ [email protected]
1982 ssh transfer
1983 sftp
1984 pwd
1985 ssh [email protected]
1986 ssh [email protected]
1987 sudo apt get-update && sudo apt-get upgrade
1988 sudo apt-get update && sudo apt-get upgrade
1989 ububtu --version
1990 ubuntu --version
1991 chdsk
1992 lsb_release -a
1993 uname -mrs
1994 sudo apt list --upgradable
1995 sudo apt upgrade
1996 exit
1997 cd Documents/microRNA_data/
1998 ls
1999 history 2>ran_script.txt
2000 history &> ran_script.txt