Hello,
If the data is RNA from rat, then you will want to be using Tophat
instead of Bowtie. Otherwise the data will not be mapped as spliced the
results will be off in many ways (the fragments counts are a small
symptom of a larger problem).
You can use 'Tophat for SOLiD' on a suitable local or cloud Galaxy
instance. It is available on the Test server, but tools are not
supported here (we test/break things!) and the quotas are just 10G with
an account. But maybe is a place to do a small trial run before
committing to a cloud server.
http://getgalaxy.org
http://usegalaxy.org/cloud
http://usegalaxy.org/toolshed
More about RNA-seq is in our wiki and public server, including link-outs
and tutorials, you can get started here:
Example ? RNA-seq analysis tools:
http://wiki.galaxyproject.org/Support#Interpreting_scientific_results
See RNA-seq examples: http://wiki.galaxyproject.org/Learn#Other_Tutorials
Best,
Jen
Galaxy team
On 11/20/13 6:09 AM, Ly, Dao wrote:
Hi
I have been trying to analyze a rat Solid SRA but I encountered a
problem: cufflinks gave me 0 RPKM in all genes. Here is my workflow
1. Get data with EBI SRA: sent the fastaq file directly to galaxy
2.Fastaq groomer
3.Mapped with bowtie for Solid (paire-ended) with the built- in index
rat rn5 as reference genome
4.Sam to Bam the bowtie mapping result
5.Cufflinks the bam file
All RPKMs of gene expression and transcript expression have a 0 value
even thought the RPKM status is OK. I used default setting for all
jobs. Am I missing something? Any help, suggestion will be greatly
appreciated. Thank you very much
Best regards
Dao
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Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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
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use the Galaxy Development list:
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