Hi Ateequr,

I sent you a reply for this question when you asked me directly last week, but perhaps this got missed. The mapping step for you data is OK. The problem comes up when Cufflinks is used with the bacterial (circular) genome with your current parameter settings.


As I mentioned, there has been some limited discussion about RNA-seq tools and parameters for circular genomes on this mailing list, but we recommended seqanswers.com or the tool authors as the best resources for this specific type of analysis advice.

To search prior Q/A on a Galaxy mailing list:
http://galaxy.psu.edu/search/mailinglists/

To reach the tool authors:
tophat.cuffli...@gmail.com
http://cufflinks.cbcb.umd.edu
http://cufflinks.cbcb.umd.edu/faq.html

Others are also welcomed to offer more advice directly as replies to this thread,

Best wishes for your project,

Jen
Galaxy team

On 3/2/12 6:57 AM, Ateequr Rehman wrote:
Dear Galxy admin and user

I have generated BAM file from my RNa seq data by using Bowtie with
custom reference, followed by Filter SAM and SAM to BAM connversion, i
wish to run cufflink, but its just givinbg me emty file,
any suggestion,
how to proceed
Ateequr Rehman
House No. 2 ground floor
Blauenstr. 10
79115 Freiburg im Breisgau


___________________________________________________________
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:

   http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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:

 http://lists.bx.psu.edu/

Reply via email to