Showing both strands in IGV, or if not possible what genome viewer is good for strand specific experiments?
1
1
Entering edit mode
9.2 years ago
Niek De Klein ★ 2.6k

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 • 5.1k views
ADD COMMENT
1
Entering edit mode
9.2 years ago
Zaag ▴ 870

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

ADD COMMENT

Login before adding your answer.

Traffic: 951 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6