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@sashaphanes
Created October 17, 2012 21:11
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convert .txt files to .fastq format
#!/usr/bin/perl -sw
# sample inputs:
#ILLUMINA-A93428 66 1 1 7848 1267 CGATGT 1 ATGTTGGCTGGCGGTGAAATAAATCTCAAACGTACCTGTTACAAAATTGTGTTAATCCTTTCAGATTCGCAG ggggggggggggggcfdffdgggfefffffcfcffcccacBeddddded_cffefgggggBBBBBBBBBBBB chrX.fa 122287709 R 40C21GAC7 269 Y
# output for sample input:
#@ILLUMINA-A93428:66:1:1:7848:1267:#CGATGT/1
#ATGTTGGCTGGCGGTGAAATAAATCTCAAACGTACCTGTTACAAAATTGTGTTAATCCTTTCAGATTCGCAG
#+ILLUMINA-A93428:66:1:1:7848:1267:#CGATGT/1
#ggggggggggggggcfdffdgggfefffffcfcffcccacBeddddded_cffefgggggBBBBBBBBBBBB
# command line:
# perl txtToFastq.pl < sampleInput.txt > output.fastq
while (<>){
chomp;
my @parts = split (/\s+/, $_);
print "@","$parts[0]:$parts[1]:$parts[2]:$parts[3]:$parts[4]:$parts[5]:#$parts[6]/$parts[7]\n";
print "$parts[8]\n";
print "+","$parts[0]:$parts[1]:$parts[2]:$parts[3]:$parts[4]:$parts[5]:#$parts[6]/$parts[7]\n";
print "$parts[9]\n";
}
@wakimchris
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is there a way to convert from fastq to txt ?

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