Question

dividing fastq file into 2 separate files

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6.5 years ago

abel.arensberg • 0

I have RNAseq data for both strands. how can I separate 2 strands from each other and make 2 fastq files? one for forward and one for reverse.

RNA-Seq • 1.4k views

ADD COMMENT • link updated 6.5 years ago by kk.mahsa ▴ 140 • written 6.5 years ago by abel.arensberg • 0

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you can use SRAtoolkit to do that

ADD REPLY • link 6.5 years ago by kk.mahsa ▴ 140

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No you can't use SRAtoolkit for the purpose OP is asking about.

ADD REPLY • link 6.5 years ago by GenoMax 141k

score 0 · Answer 1 · 2017-11-01

You first have to align the data first and then you can use splitsam.sh tool from BBMap suite to separate reads mapping to two strands. You will need to be mindful of multi-mappers, secondary alignments etc (if you have paired-end data). Finally use reformat.sh tool to recover the fastq files.

splitsam.sh mapped.sam plus.sam minus.sam unmapped.sam
reformat.sh in=plus.sam out=plus.fq
reformat.sh in=minus.sam out=minus.fq rcomp