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armintoepfer/reverse_transcribe_fastq.awk

Created October 21, 2013 00:05
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Reverse transcribe FASTQ with AWK, one-liner
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reverse_transcribe_fastq.awk
awk 'BEGIN {FS=""} {if (NR%4 == 2) { for (i = NF; i >= 1; i = i - 1) { if (x == "A") { printf "T"; } else if ($i == "C") { printf "G";} else if ($i == "G") { printf "C";} else if (x == "T") { printf "A";} else if (x == "N") { printf "N";} } printf "\n"; } else print $0 }' input.fastq > rt.fastq
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