Question: how to visualize a few hundreds RNAseq samples in IGV/GenomeBrowser
gravatar for shirley0818
4.6 years ago by
United States
shirley081890 wrote:

Hi All,

I have been using IGV tool to visualize my RNASeq data from a few samples by creating a .tdf file for each sample.

Now I have 100 samples from Group A, and another 100 samples from Group B. I have identified genes differentially expressed between these two groups.

Now I would like to view these genes using IGV or other tools to see the read difference between Group A and B. Can I just create 1 tdf/wig file by merging all 100 bam files of Group A, and create another tdf/wig file for Group B, then load in IGV/Genome Browser to view those candidate genes?

Many thanks,

rna-seq • 1.6k views
ADD COMMENTlink modified 4.6 years ago by chuanbao1230 • written 4.6 years ago by shirley081890

Yes you can, although I am not sure what you mean by 'read difference'.

ADD REPLYlink written 4.6 years ago by rens.holmer20
gravatar for chuanbao123
4.6 years ago by
chuanbao1230 wrote:

I am also a new user of IGV. As far as I know, the IGV snapshot can only show 25 samples in a single figure. To do that you need to extract the information (for faster loading) of the candidate genes and load them by a batch file.(

ADD COMMENTlink written 4.6 years ago by chuanbao1230

Thank you for your reply. But I am not interested in visualizing all 200 samples in IGV. What I would like to see is the overall read differences between Group A and Group B.

ADD REPLYlink written 4.6 years ago by shirley081890
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2533 users visited in the last hour