dividing fastq file into 2 separate files

Question

[abel.arensberg]

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.

[kk.mahsa]

you can use SRAtoolkit to do that

[GenoMax]

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

Answer 1

[GenoMax]

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