-
Notifications
You must be signed in to change notification settings - Fork 0
/
hello.world.sh
78 lines (46 loc) · 2.39 KB
/
hello.world.sh
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
#!/bin/sh
# hello.world.sh
# BiX - beta
#
# Created by BiX on 11/1/17.
#
# housekeeping ---------------------------------------------------------------------------------------------------
export PATH="/network/rit/lab/ahmedlab/bin/anaconda2/bin/:$PATH"
export PATH="/network/rit/lab/ahmedlab/bin/:$PATH"
export PATH="/network/rit/lab/ahmedlab/bin/homebrew/bin/:$PATH"
export PATH="/network/rit/lab/ahmedlab/bin/bcl2fastq/usr/local/bin/:$PATH"
# rename the fastq files to append PI name and PIN (Project Identifier Number) ------------------------------------
for i in *; do mv "$i" Morgan.Sammons.0002."$i"; done
# multiQC usage ---------------------------------------------------------------------------------------------------
/network/rit/lab/ahmedlab/bin/anaconda2/bin/multiqc ${FASTQC} \
-n Morgan.Sammons.0001.multiQC.fastqc
# awk usage -------------------------------------------------------------------------------------------------------
awk '{OFS="\t";if(NR==1) {print;} else if(NR >= 4819050 && NR <= 4835639) {print;} else {$1="chr"$1; print;}}'
# unzip .rpm files
rpm2cpio ../file.rpm | cpio -idmv #extract mkdir preserve verbose
# homer usage -----------------------------------------------------------------------------------------------------
makeUCSCfile S1.tag.dir/ -o auto -fsize 5e7 -res 1 -color 106,42,73 -style chipseq
# homer configure.pl script location
/network/rit/lab/ahmedlab/bin/anaconda2/pkgs/homer-4.9.1-pl5.22.0_5/share/homer-4.9.1-5
# count lines of fastq.gz files ------------------------------------------------------------------------------------
for i in ./*; do echo 'working with' $i; zcat $i | wc -l ; done
# rename the fastq files to append PI name and PIN (Project Identifier Number)--------------------------------------
for i in *; do mv "$i" Morgan.Sammons.0002."$i"; done
# use cases coreData -----------------------------------------------------------------------------------------------
for D in /network/rit/lab/ahmedlab/projects/Morgan.Sammons.0003/Morgan.Sammons.0003.fastq/*; do
if [ -d "$D" ]; then
cd "$D"
mv * ..
cd ..
fi
done
# For single end reads!
cd /network/rit/lab/ahmedlab/projects/Morgan.Sammons.0001/coreData/loop2/ &&
for dir in Morgan.Sammons.0001*/; do
for r in R1; do
outfile=${dir%/}_${r}.fastq.gz
glob=*_${r}_*.fastq.gz
cat "$dir"/$glob > "$dir/$outfile" &&
rm -f "$dir"/$glob
done
done