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Convert all Illumina qseq.txt files into fastq files, organized by lane

/ Published in: Bash
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  1. for ((x=1;x<=8;x+=1)); do for ((y=1;y<=3;y+=1)); do cat s_"$x"_"$y"_*_qseq.txt | awk -F '\t' '{gsub(/\./,"N", $9); if ($11 > 0) printf("@%s_%04d:%s:%s:%s:%s#%s/%s\n%s\n+%s_%04d:%s:%s:%s:%s#%s/%s\n%s\n",$1,$2,$3,$4,$5,$6,$7,$8,$9,$1,$2,$3,$4,$5,$6,$7,$8,$10)}' > s_"$x"_sequence.fastq; done; done

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