1812 days ago
1616 days ago
Bash script to download SRA file !
...a particular sequencing run ID fastq-dump --split-files SRR1770413 #SRA stor...hings into FASTQ for further processing. The --split-files part of the command ens...R/SRR177/SRR1770413/SRR1770413.sra sra-dump --split-files SRR1770413.sra1571 days ago
To convert just one specific read group to fastq
...Store the data in the reads folder. mkdir -p reads # Download the SRR data for each cat selected.txt | parallel fastq-dump -O reads -X 1000 --split-files {} # Create a direct...1554 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1412 days ago
Perl script to run awk inside perl
...switches $, = ' '; # set output field separator $\ = "\n"; # set output record separator while () { chomp; # strip record separator @Fld = split(' ', $_, -1); if ($awk) { $...1175 days ago
Split the string with underscore and store values in array with AWK !
more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}' #Other extraction more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}'> enriched_ids_list awk 'NR==FNR{tgts[$1]; next} $1 in tgts' enriched_ids_list result/GO.out > enriched_GO.out.xls906 days ago
Perl script to rename the fasta file !
#Script #1 #!/usr/bin/perl -w use strict; #USAGE #perl extractPattern.pl kmerfasta > uniref100_result_broad my %kHash; local $/ = '>'; my $infile2 = "$ARGV[0]"; # Kmer fasta open( FH2, '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.fasta863 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here, N=500), by using the foll...: http://genometools.org/, which has the following simple command: gt splitfasta -numfiles 10 multi.fasta835 days ago