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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