Showing both strands in IGV, or if not possible what genome viewer is good for strand specific experiments?
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5.9 years ago
Niek De Klein ★ 2.5k

I have strand specific RNA seq data that I would like to view in IGV or a similar genome browser (with fast scrolling/zooming). I am looking for something like the (a) part of this figure (from RNASeqBrowser):

Where the positive strand is above the line, and negative strand is below the line. At the moment I use IGV and have one track for the positive strand and one track for the negative strand, but this gets confusing when comparing multiple samples.

What I could find is that IGV does not have the ability to do this but the threads that I could find are a few years old, so my questions are:

1. Is it already possible to view strand specific data in IGV like above figure? and if not

2. What is a good browser with fast scroll/zoom speeds that can do this?

IGV genome-browser • 3.5k views
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1
Entering edit mode
5.9 years ago
Zaag ▴ 800

I think this can do what you want: http://goldenhelix.com/GenomeBrowse/

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