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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: