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: