how to visualize rna-seq coverage track in igv?

Question

[Zee_S]

Hello biostars community,

how does one visualize an rna-seq coverage track alongside chip-seq bigwig tracks in igv?

the problem i have is that, when i zoom into the rna-seq coverage track (becaus eit is a bam file), i lose the resolution on my bigwig tracks (too zommed in) and i can no longer visualize everything in parallel.

the other question is that, coverage track is not normalized, how do i normalize it so that two rna-seq coverage tracks can be compared to one another for assessing the difference in the level of expression?

many thanks!

[Asaf]

You can display bam files in larger zoom out than the default. Somewhere in the settings.

[Zee_S]

what do you mean by larger zoom out? can you please elaborate?

[Asaf]

You can redefine the point it writes "Zoom in to see alignment", make it wider (will slow down obviously), can't find where at the moment. As for you second question you can right click the coverage track and unmark "Autoscale" and click on "Set Data Range" to set the desired range.

Answer 1

[jared.andrews07]

As for your second question, the short answer is that you can't.

Using coverage tracks (even if normalized via RPKM/FPKM/what have you) to try to determine differential gene expression has all sorts of issues. They should only be used as a visual aid to show expression changes between samples that were identified with robust, statistically-backed methods using gene counts like edgeR, DESeq2, limma, etc. If you just want them to serve as that sort of visual aid, then deepTools is an excellent option for creating depth/control-normalized tracks.

[Zee_S]

this is very useful feedback thank you very much.

[Zee_S]

Hello! I would like to come back to this post to ask: when we visualise RNA-seq tracks, do you include both unique and multi mappers? or why is it that some people only use unique mappers? which is the correct way?

Thank you!