Hello Jianguang, The file "Cuffdiff on data <...>: splicing differential expression testing" is described here: http://cufflinks.cbcb.umd.edu/manual.html#splicing_diff --> 5) Differential splicing tests - splicing.diff The CuffMerge file GTF output also has the TSSID attribute, in the 9th field. These were the exons considered when the differential expression testing was done and the genomic coordinates are in this file. http://cufflinks.cbcb.umd.edu/manual.html#merger_output --> a GTF file The original assembled transcripts from Cufflinks can be added to a visualization along with the reference annotation GTF data. You could visualize the Tophat output as well (accepted hits, junctions, etc.), it just depends on how much detail you want. Hopefully this helps, Jen Galaxy team On 8/21/12 11:01 AM, Du, Jianguang wrote:

Dear All,

I have run programs from Tophat to Cuffdiff of Galaxy to look for the difference in alternative splicing events between cell types. However I do not know how to find the detail information (such as the sequence and the genomic coordinates) of the alternatively spliced part of a given gene. I looked at the data of Cuffdiff ouput " splicing differential expression testing", there is no column showing the position of alternatively spliced region. Please help to solve this problem.

Thanks in advance.

Jianguang Du

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