Hi Benjy, To extract unmapped reads from a SAM file in Galaxy, you can use 'Filter SAM' ('NGS: SAM Tools' -> 'Filter SAM'). Add a 'flag' and use the 'The read is unmapped' type, then set the state for this flag to 'Yes'. This should return a SAM file with your unmapped reads. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Thu, Nov 7, 2013 at 1:22 PM, Benjamin Osei-agyeman < benjy_osei@yahoo.co.uk> wrote:

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:

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