Hello Els, For initial versions, the RNA-seq pipeline's tool authors did not provide any counts of this type (on purpose). The latest version does include a type of count (alternate to the normalized FPKM counts) and it is described at the Cufflinks web site, under the tool Cuffdiff -> Count Tracking. This is not yet incorporated into Galaxy. http://cufflinks.cbcb.umd.edu/faq.html#numfrags http://cufflinks.cbcb.umd.edu/manual.html If your reads are mapped a reference genome, and you have transcripts mapped to the same reference genome, you can compare the overlapping coordinates and generate counts. This will assign reads to more than one transcript - "raw" counts based only on overlap. Tools to use for this purpose can be found in the group "BEDTools" or you could covert the SAM/BAM alignments to interval format and use the tools in " Operate on Genomic Intervals" and the tool "Group" as needed. Hopefully this helps, Jen Galaxy team On 5/17/13 2:11 AM, Els Willems wrote:

Dear all,

I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the Tophat-Cufflinks pipeline in Galaxy, but I would like to obtain a raw count of the number of mappings per transcript. I have not found a way to do this in Galaxy, is this possible? Thank you very much.

Regards, Els

--- Ir. Els Willems KU Leuven Department of Biosystems Division Livestock - Nutrition - Quality Laboratory of Livestock Physiology Kasteelpark Arenberg 30 bus 2456 B - 3001 Heverlee T (+32) 016 32 17 29 F (+32) 016 32 19 94

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