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

; * From: * Jeremy Goecks ; > * To: * Benjamin Osei-agyeman ; > * Cc: * ; > * 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. >

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 shoul

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 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 to the genome? > >

[galaxy-user] Contents of a SAM file

Hi What are the contents of a SAM file after Bowtie has been run? Does it contain all reads or only those reads mapped to the genome? Thanks Benjy___ The Galaxy User list should be used for the discussion of Galaxy analysis and other feat