How can I load GEO-datasets in an UCSC genome browser?

21 February 2014 1 7K Report

I would like to view some interesting data from the GEO database in UCSC genome browser. It worked fine for me with some wig.gz files. However, most files that I tried yesterday failed, for example http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34261

I tried to upload the wig.gz file for this sample (genome: mouse, assembly: mm8) but received the following error:

Error File 'GSM846042_MLL_Nter.a_m_1_best_strata.mm8.wig.gz' - track load error (track name='ct_MLLNter_7154'):

Found start=0 at line 46243375, the first chrom position is 1, not 0

What am I doing wrong?

Puck Nijhuis

Thank you for your answer! The dataset that I tried to upload is a mouse-dataset. Since their is mm8 in the filename, I used mm8 as reference genome...but it is not working..

Anybody else a suggestion?

Is there maybe a website with information how to load GEO- datasets, with all the different extensions .wig.gz, .raw, etc?

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