Re: [galaxy-user] SAM to GFF ?

2011-02-18 Thread Peter 
On Fri, Feb 18, 2011 at 12:08 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote:
 Hi,
 is there an easy way to use Galaxy to convert SAM to GFF?
 thx,
 Felix

How so?

SAM/BAM shows you where your reads map, GFF is used for
annotation (e.g. where the genes are and what they may do).

Are you talking about using SAM/BAM transcriptome mapping
(RNA-Seq) for gene finding?

Peter
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Re: [galaxy-user] SAM to GFF ?

2011-02-18 Thread Peter 
On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote:

 Hi Peter,
 thx for the reply.
 You're right I want to display mapped RNA seq data in gBrowse.
 Currently I have the data in SAM format.
 Maybe I can figure out a trick using the text manipulation tools.
 thx,
 Felix

You forgot to CC the mailing list. If you want to use the data in
GBrowse then why not use SAM/BAM directly? I've not tried
it yet but I understand GBrowse can display BAM files... best
asking on their mailing list if you need more details. This
doesn't involve Galaxy directly though...

Peter
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Re: [galaxy-user] SAM to GFF ?

2011-02-18 Thread vasu punj 
I have used IGV with the Bam file and one ha sto generate index file which can 
be done in IGV, it work well. Gbrowser should also be OK. I think new version 
of IGV provide lot more features than previous one
Vasu.


--- On Fri, 2/18/11, Peter biopyt...@maubp.freeserve.co.uk wrote:


From: Peter biopyt...@maubp.freeserve.co.uk
Subject: Re: [galaxy-user] SAM to GFF ?
To: Felix Hammer hamm...@cip.ifi.lmu.de
Cc: galaxy-user@lists.bx.psu.edu
Date: Friday, February 18, 2011, 8:09 AM


On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote:

 Hi Peter,
 thx for the reply.
 You're right I want to display mapped RNA seq data in gBrowse.
 Currently I have the data in SAM format.
 Maybe I can figure out a trick using the text manipulation tools.
 thx,
 Felix

You forgot to CC the mailing list. If you want to use the data in
GBrowse then why not use SAM/BAM directly? I've not tried
it yet but I understand GBrowse can display BAM files... best
asking on their mailing list if you need more details. This
doesn't involve Galaxy directly though...

Peter
___
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. 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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