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repeat_masking.sh
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## Repeat masking for gene prediction of contaminant reduced crab assemblies
# remove contig which does not contain any G nucleotides (i.e., ATC only)
cat Mani_v1.6.fa | paste - - | grep -v -F ptg016427l | tr "\t" "\n" > Mani_v1.7.fa
# de novo repeat identification using RepeatModeler
BuildDatabase -name Mani Mani_v1.7.fa
RepeatModeler -database Mani -pa 24 -LTRStruct
# annotation and masking using RepeatMasker
RepeatMasker -pa 24 -lib Mani-families.fa Mani_v1.7.fa -xsmall
#==================================================
#file name: Mani_v1.7.fa
#sequences: 7486
#total length: 923773821 bp (923773821 bp excl N/X-runs)
#GC level: 38.24 %
#bases masked: 542843944 bp ( 58.76 %)
#==================================================
# number of length percentage
# elements* occupied of sequence
#--------------------------------------------------
#Retroelements 251001 100201730 bp 10.85 %
# SINEs: 0 0 bp 0.00 %
# Penelope 5898 1578852 bp 0.17 %
# LINEs: 192945 75638857 bp 8.19 %
# CRE/SLACS 82 59106 bp 0.01 %
# L2/CR1/Rex 80012 26418587 bp 2.86 %
# R1/LOA/Jockey 25188 20240227 bp 2.19 %
# R2/R4/NeSL 1297 1072855 bp 0.12 %
# RTE/Bov-B 57721 17970553 bp 1.95 %
# L1/CIN4 1082 270928 bp 0.03 %
# LTR elements: 58056 24562873 bp 2.66 %
# BEL/Pao 0 0 bp 0.00 %
# Ty1/Copia 22421 3488085 bp 0.38 %
# Gypsy/DIRS1 35279 21026105 bp 2.28 %
# Retroviral 356 48683 bp 0.01 %
#
#DNA transposons 78739 25485922 bp 2.76 %
# hobo-Activator 14775 3311690 bp 0.36 %
# Tc1-IS630-Pogo 26736 10293149 bp 1.11 %
# En-Spm 0 0 bp 0.00 %
# MuDR-IS905 0 0 bp 0.00 %
# PiggyBac 4075 3425279 bp 0.37 %
# Tourist/Harbinger 2970 1758172 bp 0.19 %
# Other (Mirage, 6819 2465531 bp 0.27 %
# P-element, Transib)
#
#Rolling-circles 1630 265603 bp 0.03 %
#
#Unclassified: 1286958 329235969 bp 35.64 %
#
#Total interspersed repeats: 454923621 bp 49.25 %
#
#
#Small RNA: 9658 1992403 bp 0.22 %
#
#Satellites: 1114 148604 bp 0.02 %
#Simple repeats: 1020918 77734145 bp 8.41 %
#Low complexity: 75865 7779568 bp 0.84 %
#==================================================
# repeat the above steps for the second species
# de novo repeat identification using RepeatModeler
BuildDatabase -name Cinc Cinc_v1.5.fa
RepeatModeler -database Cinc -pa 24 -LTRStruct
# annotation and masking using RepeatMasker
RepeatMasker -pa 24 -lib Cinc-families.fa Cinc_v1.5.fa
#==================================================
#file name: Cinc_v1.5.fa
#sequences: 9390
#total length: 1491129859 bp (1491129859 bp excl N/X-runs)
#GC level: 39.63 %
#bases masked: 1115386838 bp ( 74.80 %)
#==================================================
# number of length percentage
# elements* occupied of sequence
#--------------------------------------------------
#Retroelements 256439 202879600 bp 13.61 %
# SINEs: 0 0 bp 0.00 %
# Penelope 12476 5778472 bp 0.39 %
# LINEs: 209515 149410244 bp 10.02 %
# CRE/SLACS 428 866820 bp 0.06 %
# L2/CR1/Rex 64027 38415218 bp 2.58 %
# R1/LOA/Jockey 42758 61460597 bp 4.12 %
# R2/R4/NeSL 1461 915305 bp 0.06 %
# RTE/Bov-B 52879 25024372 bp 1.68 %
# L1/CIN4 20 2113 bp 0.00 %
# LTR elements: 46924 53469356 bp 3.59 %
# BEL/Pao 1719 1775059 bp 0.12 %
# Ty1/Copia 580 922309 bp 0.06 %
# Gypsy/DIRS1 42230 49701106 bp 3.33 %
# Retroviral 2395 1070882 bp 0.07 %
#
#DNA transposons 92610 29283451 bp 1.96 %
# hobo-Activator 10113 2858343 bp 0.19 %
# Tc1-IS630-Pogo 20527 5664433 bp 0.38 %
# En-Spm 0 0 bp 0.00 %
# MuDR-IS905 0 0 bp 0.00 %
# PiggyBac 2261 2582346 bp 0.17 %
# Tourist/Harbinger 5922 4384674 bp 0.29 %
# Other (Mirage, 18406 4784824 bp 0.32 %
# P-element, Transib)
#
#Rolling-circles 3964 986700 bp 0.07 %
#
#Unclassified: 1384990 806688934 bp 54.10 %
#
#Total interspersed repeats: 1038851985 bp 69.67 %
#
#
#Small RNA: 4811 1737726 bp 0.12 %
#
#Satellites: 2127 250510 bp 0.02 %
#Simple repeats: 799000 67321864 bp 4.51 %
#Low complexity: 57159 6238053 bp 0.42 %
#==================================================