split oligo reads by strand

Question

[crazyscientist]

Hello,

I have mapped the fastq files with BWA tool which gave me .bam files. Further, I would like to split this bam file on the basis of forward and reverse strand. Which tool is best for doing this process. Any tool available on Galaxy? Thanks in advance.

[GenoMax]

If this is a request specific for galaxy then you should post this over at: https://help.galaxyproject.org/

Otherwise use answers in this thread : Single-end strand specific Rna-Seq: how to separate alignments by strand

[ATpoint]

As you tagged RNA-seq I hope you know that BWA does not support spliced alignments. What organism are you working with? Do you have stranded data that reliable distinguish the strands?

[crazyscientist]

I am aligning with BWA before splitting. I am working with Bacillus genome. Yes, I have stranded data. Thank you.

[ATpoint]

Ok, just wanted to be sure because we often see users here that do not know the difference between standard DNA-seq alignment and RNA-seq. As for your problem, samtools view is the way to go as suggested in the post that genomax linked.