How to get GSE data into IGV

Question

[michael.laz]

Hi all,

I am trying to view a GSE ChIP-Seq data file into IGV but when I download the GSE, it is not in a format that IGV can read. I do not see on option of the GEO Accession viewer that is able to convert the file into something that IGV can read. How can I view this file in IGV?

Thanks in advance!

Answer 1

[heskett]

I'm not super familiar with GSE, but you should realize that IGV will readily accept BAMs, BEDs, and VCFs. If you want to view ChiP-seq peaks in IGV, it likely needs to be in a BED (or BigWig) format that specifies the chromosome, position, and "score" of each chip signal. So perhaps do some searching on how to convert GSE to BED, or work on writing a small script that can convert it.