Divide reads to shorter reads in Fastq file
Hi
Is there package/software/python module that takes each read in Fastq file and divide it to 2 shorter reads? In my case, take 150 bp read and divide into 75 bp 2 reads.
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Ram
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written
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Ahiad Chen Zion •
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written
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Ahiad Chen Zion •
2 answers
gunzip -c in.fa.gz | paste - - - - | awk -F '\t' '{L=length($2);printf("%s\n%s\n+\n%s\n",$1,substr($2,1,L/2),substr($4,1,L/2)); printf("%s\n%s\n+\n%s\n",$1,substr($2,L/2+1),substr($4,L/2+1));}'
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Pierre Lindenbaum
Using reformat.sh from BBMap suite (two steps):
reformat.sh -Xmx2g in=read.fastq.gz out=left_75bp.fastq.gz forcetrimright=74
reformat.sh -Xmx2g in=read.fastq.gz out=right_75bp.fastq.gz forcetrimleft=74
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