how to visualize a few hundreds RNAseq samples in IGV/GenomeBrowser

Question

[shirley0818]

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,
Shirley

[rens.holmer]

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

Answer 1

[chuanbao123]

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.(http://www.broadinstitute.org/igv/batch)

[shirley0818]

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.