Re: [galaxy-user] Contents of a SAM file

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: Hi What are the contents of a SAM file after Bowtie has been run? Does it contain all reads or only those reads mapped

Re: [galaxy-user] Contents of a SAM file

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 ___ The Galaxy User list

Re: [galaxy-user] Contents of a SAM file

-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