Generate a separate bigwig tracks for each strand.

[ggrimes]

Is your feature request related to a problem? Please describe

The nf-core/rnaseq version 3.0 pipeline produces only one strand of coverage depending on the strandedness provided.

e.g.

bedtools \ genomecov \ -ibam sample.sorted.bam \ -bg \ -strand - -du \ -split \ | bedtools sort > HDox_R1.bedGraph

Describe the solution you'd like

Could this be changed to include coverage for both strands in separate files?

Describe alternatives you've considered

Maybe the bigwig files could be generated using deeptools bamCoverage

Additional context

[drpatelh]

This should be fixed now @ggrimes ! Be great if you can test it out by using the code on the dev branch! I went for the simple approach of not using any normalisation for now but the tracks should be properly separated by strand.

[ggrimes]

I have checked the bigwig file produced using the test profile and the dev branch and it is producing the correct bigwigs files for each strand. This issue can be closed. An issue for later would be to options to specify the normalization for the bigwig tracks.

[ChristopherBarrington]

@drpatelh The two strand files are named sense and antisense but look as though they are based on genome strand rather than transcription direction. Perhaps forward/reverse would be more intuitive naming scheme, unless I have misunderstood something, since sense/antisense has a specific meaning in RNA-seq?

Screen shot attached shows high expression in 'sense' or 'antisense' depends on transcription direction. This is PE data - I'm not sure how that is resolved when choosing a strand.