Thanks a lot, If i want to extract the unmapped reads from the SAM file after bowtie has run do I have to use Samtools or can this be done straightaway using galaxy? What command should I use? Thanks Benjy

---

From: Jeremy Goecks <jeremy.goecks@emory.edu>;
To: Benjamin Osei-agyeman <benjy_osei@yahoo.co.uk>;
Cc: <galaxy-user@lists.bx.psu.edu>;
Subject: Re: [galaxy-user] Contents of a SAM file
Sent: Thu, Nov 7, 2013 1:12:44 PM

All reads are in the SAM file; you can filter to remove unmapped reads as needed. J. On Nov 7, 2013, at 5:36 AM, Benjamin Osei-agyeman <benjy_osei@yahoo.co.uk> wrote:

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/