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_o...@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.goe...@emory.edu>; > * To: * Benjamin Osei-agyeman <benjy_o...@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_o...@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/ >
___________________________________________________________ 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/
