Visualisation Of Geo Database Data In Gbrowse

Question

[Gvj]

How could I use the raw files from NCBI GEO database to visualizes in Gbrowse, something like discussed in http://biostar.stackexchange.com/questions/1459/how-do-i-set-up-gbrowse-for-comparative-coverage ( ie in wiggle_xyplot)? The problem I am facing is each entries ( eg: GSE8169, GSE20176 ) in ftp are in different format (.soa ,.cel, txt etc) which I am not familiar with. Do you have any suggestion for me how can i convert them to gff/wig in order to use in? Its my first time I am using chip-chip/seq data. my final objective is to visualize the raw data of different studies together.

Thanking you in advance, Gvj

Answer 1

[Charles Warden]

I don't think there is a universal answer for your question.

The specific GEO accessions are for ChIP-chip and ChIP-Seq datasets. In these cases, I would probably recommend using a peak calling algorithm (such as MAT) to call peaks for each sample. You can then create a .bed file that can be probably be visualized in Gbrowse (I know it will work in IGV and the UCSC Genome Browser).

For the ChiP-Seq data, you can create a pileup file using samtools, which you could convert to a .wig file. You could arguably do something similar with some level of processed data prior to peak calling, but I don't think the raw ChIP-chip and ChIP-Seq values will be comparable. Thus, I would recommend looking for overlapping .bed tracks instead.