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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