How to get different colors on coverage tracks in IGV · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

How to get different colors on coverage tracks in IGV

Hi, I am comparing different bam files in IGV and want to display only the coverage tracks in different colors, kind of like this. However, I couldn't find an option to color the coverage track in IGV. And if I export to .svg and import in Illustrator it is hard to select only the elements of the coverage track and then change colors. Any suggestions appreciated!

igv rna-seq

• 6,719 views • link

updated 9.9 years ago by Carlo Yague

• written 9.9 years ago by jon.brate

1 answer

Answer on the IGV online manual.

• 1 views • link

written 9.9 years ago by Carlo Yague

Thanks! I was using version 2.3.68 and this option was not available. But in 2.3.80 it is! Thanks!

• 1 views • link

written 9.9 years ago by jon.brate

Log in to answer this question.

More posts like this

How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV v…
written 4.6 years ago by sir.outman •

Dear fellows: I have some ATAC bam files(A549 in drugged and control condition) which have different sequence depths that need to convert to bigwig. The …
Visualize B-allele frequency on IGV for 2 samples
written 7.8 years ago by German.M.Demidov

Dear All, I have a non-standard task - visualize B-allele frequency tracks for 2 samples in 1 track in IGV. It is not difficult to …
WGCNA module interpretation question
written 8.0 years ago by Anny •

I am using WGCNA to generate gene co-expression network. I am confused about the how to interpret gene module colors. My understanding is, different modules …
IGV not highlighting possible variants
written 8.1 years ago by francois •

Surely this is trivial, but I have looked everywhere and I cannot find the answer... IGV sometimes does not want to highlight the possible variants …
cufflinks with reference annotation, FPKM for a gene
written 10.9 years ago by tonja.r

I run a cufflinks (2.2.1) with annotated exons (I do not want t count intron reads) and got the following gene tracks and isoform tracks. …
Showing both strands in IGV, or if not possible what genome viewer is good for strand specific expe…
written 10.9 years ago by Niek De Klein

<p>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 …
How To Display Eight Samples As Ucsc Custom Tracks
written 12.8 years ago by Nitin •

<p>I have 4 samples in each grp in untreated vs treated grp. I want to display all this data of two grps (8 samples) in …
How To Display Reads Profiling By Sense And Antise Separately Using Gbrowse?
written 14.4 years ago by Zhlingl •

<p>hello, i am using Gbrose to visualise NGS data, and i want to show the expression number of sense mapping reads and antisense mapping reads …
How To Create 'Grass-Like' Graphs (Barcharts) In Ucsc Browser Tracks?
written 15.4 years ago by Giovanni M Dall'Olio

<p>Some of the tracks in the UCSC browser are shown as spiky or 'grass-like' charts:</p> <p><img src="http://img689.imageshack.us/img689/5248/hgtwww50818d7360.png" alt="alt text"/></p> <p>I can not find the documentation …
How Do I Set Up Gbrowse For Comparative Coverage?
written 16.2 years ago by Jeremy Leipzig

I am using the gbrowse2 samtools setup to display short read data in terms of coverage plots. Gbrowse is selecting different ranges or limits for …