Hi Yan,
I suspected that this was what you were originally asking, but then
reconsidered when I read the subject line again. This is because one of
the functions of Cufflinks is to do what you are asking - it brings
together mapped RNA-seq data to produce transcript/genes based on either
read overlap alone or read overlap plus overlap with reference
annotation (GTF reference annotation).
As far as I know, modifying the RNA-seq input by assembling it first or
by collapsing redundancy would change the nature of the experiment.
Reviewing the Cufflinks documentation will help with understanding how
this processing was designed to work with the expected inputs:
http://cufflinks.cbcb.umd.edu/manual.html
Assembly is not available on Galaxy Main, but there are other options.
For general RNA-seq assembly purposes (not advised for Cufflinks, at
least for the RNA-seq input), you could run a local or cloud instance
(http://getgalaxy.org) and consider Trinity (alpha). This was announced
in the May News Brief:
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_05_11#Tools
There are also tools available from the Tool Shed to consider. Search
for 'assembly' or 'trinity' - but be sure the tool is for RNA and not
DNA. Tools here are supported by the tool wrapper/authors themselves -
the contact information is with each repository.
http://toolshed.g2.bx.psu.edu/
As an aside, using Bowtie is non-standard (TopHat is preferred, unless
you are working with a genome that has an unspliced transcriptome). I
was making the assumption that this was the case with your data, but I
did want to mention it in case it wasn't clear. If the desire to
assemble is related to the use of a circular genome, then you may want
to contact the tool authors at their support email to see what protocol
advice is available: tophat.cuffli...@gmail.com. Posting back any
replies, creating a tutorial, or adding a page in the Galaxy wiki on the
subject would be most welcome - other Galaxy users would likely be very
interested.
Hopefully this helps,
Jen
Galaxy team
On 8/14/12 8:43 PM, Yan He wrote:
Hi Jen,
Thanks for your reply! I know this workflow. I am just wondering if there
is a tool in Galaxy to combine the reads that mapped to the same gene with
different positions before running cufflinks.
Thanks again,
Yan
-----邮件原件-----
发件人: Jennifer Jackson [mailto:j...@bx.psu.edu]
发送时间: Wednesday, August 15, 2012 11:01 AM
收件人: Yan He
抄送: galaxy-user@lists.bx.psu.edu
主题: Re: [galaxy-user] how to sort mapped data?
Hello Yan,
To sort a SAM file produced by Bowtie before using it with Cufflinks (a
requirement), please see this FAQ and workflow:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2
Best,
Jen
Galaxy team
On 8/14/12 7:33 PM, Yan He wrote:
Hi everyone,
I am working on RNA-seq data. First, I mapped the reads to the
reference transcriptome using bowtie. I found some different reads
mapped to the same gene with different positions. Before running
Cufflinks, I would like to combine the reads that mapped to the same
gene though with different positions. Is there a tool in Galaxy can
fulfill this purpose?
Any suggestion would be much appreciated. Thanks!
Yan
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Jennifer Jackson
http://galaxyproject.org
--
Jennifer 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
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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