Question: Splitting paired-end RNA-seq data in bedgraph format according to strand
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gravatar for virlana.shchuka
11 months ago by
virlana.shchuka0 wrote:

I currently have several paired-end RNA-seq datasets scaled to rpm in bedgraph format (thanks to a former biostar question post reply that was very helpful! :)).

Is it possible to work from these files as they are, and split them into two tracks, one with only positive strand reads and one with only negative strand reads? Or is it necessary to return to the original bam files to do this? Either way, how might the command lines look, and how will the fact that these are paired-end datasets influence the commands I have to use?

rna-seq • 278 views
ADD COMMENTlink written 11 months ago by virlana.shchuka0

Could you show the first 5 rows of your bedgraph-formatted files?

ADD REPLYlink written 11 months ago by cpak1981100
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