Hi Ateeq,

The BAM/SAM files can be visualized in Trackster, using your custom reference genome (the same dataset as used for Bowtie or TopHat). But, there are no Cufflinks results, and therefore nothing to visualize, due to the parameters used.


Since you are working with a bacterial genome, the parameters will need to be tuned to account for the lack of transcript splicing. The best resources for advice are likely seqanswers or the tool authors, as explained in this prior answer to another bacterial genome/RNA-seq question:
http://galaxy-users-list-archive.2308625.n4.nabble.com/Cufflinks-merging-more-than-one-transcript-on-bacterial-genomes-td4323709.html

Recently, there has been some user discussion about RNA-seq analysis and bacterial genomes on the galaxy-user mailing list. If you want to search and read through the Q&A, using our custom google search is the best way to locate the threads (but, expect to find just a few):
http://galaxy.psu.edu/search/mailinglists/

If anyone else reading this thread has help to offer, please feel free to jump in and share any working knowledge for this type of analysis.

Best wishes for your project,

Jen
Galaxy team

On 2/29/12 12:31 PM, Ateequr Rehman wrote:
hello Jennifer
Thanks a lot, here is the link

Best
ateeq


------------------------------------------------------------------------
*From:* Jennifer Jackson <j...@bx.psu.edu>
*To:* Ateequr Rehman <atee...@yahoo.com>
*Cc:* "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
*Sent:* Wednesday, February 29, 2012 9:24 PM
*Subject:* Re: [galaxy-user] Visualise data

Hi Ateeq,

Please share a link to your history so that we can provide feedback. Use
"Options -> Share or Publish", generate the share link (first button),
copy the link into a reply email, and send that back to me directly.

Also, your last few questions have been sent as replies to other
questions on the mailing list with a new subject line. This causes them
to thread/track incorrectly (and potentially be missed). When sending a
new question, please start with a brand new message, address the "to" as
"galaxy-u...@bx.psu.edu <mailto:galaxy-u...@bx.psu.edu>" and this will
reach us correctly.

Thank you and I will watch for your reply,

Jen
Galaxy team

On 2/29/12 11:30 AM, Ateequr Rehman wrote:
 > Hello Admin and users
 >
 > i wanted to visualize my data, i ran Tophat and converted sam to BAM and
 > then cufflink,
 > but totally unable to see any output data,
 >
 > any suggestion, how i could see my results
 >
 > For administrators, on my account run number 76 to 79 are the run i want
 > to visualize
 >
 >
 > Thanks
 > Ateeq
 >
 >
 > ___________________________________________________________
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support



--
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/

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