1196 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdi...4:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wfo...4:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wfo...1196 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required m...ile); #print $code; my $ae = Archive::Extract->new( archive => $file); m..._LSU_code; my $silva_LSU_ae = Archive::Extrac...1153 days ago
1151 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt989 days ago
943 days ago
Extract the values using ids !
#Awk script awk 'NR==FNR{tgts[$1]; next} $1 in tgts' file1 file2 Look: $ cat file1 11002 10995 48981 79600 $ cat file2 10993 item 0 11002 item...887 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas882 days ago
Extract fasta header with ids !
#Extract all the fasta header name with certain ids kraken --db ../../../../DATABASE/minikraken_20171019_8GB.tgz out.fa more out.fa_class.txt | grep "227859" | awk...870 days ago
Extract the sequences with IDs !
#sed -i 's/\_/ /g' Delta_seqID_from_lineage_report.txt seqtk subseq genomic.fna Delta_seqID_from_lineage_report.txt > Delta.fasta #Split the fasta in 11 equal sequences subsets pyfasta split -n 11 Delta.fasta844 days ago