How do you compare splice junctions in mm9 to genes in hg19, using TopHat2 in galaxy and UCSC genome browser?

Chris Skovgaard Ramming @Chris_Skovgaard_Ramming

03 March 2014 0 5K Report

I have some questions about bioinformatics, since it's not my strong side. I'm investigating whether some alternative splicing is occurring in the human cell line H1-hESC, using the mouse genome mm9 as starting point, since there are an alternative splicing on this location chr8:87,578,307-87,578,657 in mm9. And I need to find out if that also occurs in the H1-hESC cell line. So how do I approach the Galaxy server and the UCSC genome browser? I have uploaded my TopHat2 bed file.

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