Plot stranded RNA-seq data at gene level

Question

[boludopublico]

Dear all, I was wondering if someone would have a suggestion as to which R tool to use for publication-quality plotting of RNA-seq data; say, to show reads density at gene level. Thanks!

[GouthamAtla]

You mean as a genome browser track ?

[boludopublico]

Yes indeed. It would be nice to prepare some type of genome-browser track, but I dont want to capture an image of say SeqMonk or IGV. I would like to prepare particular genome windows in R, for example.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

You don't need to capture (by which I suppose you mean take screenshots) images from IGV. You can export them in PNG/SVG format from IGV (possibly from seq monk as well) and then work with them elsewhere.

[boludopublico]

Thanks, but I would like to use different aesthetics than SeqMonk/IGV for publication. I also had quality problems with the PNG format, at least from SeqMonk. For certain data I have been using SUSHI, but it doesn't look good for RNA-seq

[h.mon]

Maybe plotCoverage from the deepTools package can fit your needs.

[boludopublico]

Thanks. I was under the impression that this was for estimating sequencing depth. How would one go from the plotCovergage to an actual genome browser sort of track ?

[h.mon]

If you really want a genome browser sort of track, then have a look at pyGenomeTracks. The path would be to convert your bam to bigwig or bed, probably.

[boludopublico]

Aja! This looks useful, thanks