[galaxy-user] SAM to GFF ?

Hi, is there an easy way to use Galaxy to convert SAM to GFF? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and

Re: [galaxy-user] SAM to GFF ?

On Fri, Feb 18, 2011 at 12:08 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote: Hi, is there an easy way to use Galaxy to convert SAM to GFF? thx, Felix How so? SAM/BAM shows you where your reads map, GFF is used for annotation (e.g. where the genes are and what they may do). Are you talking

Re: [galaxy-user] SAM to GFF ?

On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote: Hi Peter, thx for the reply. You're right I want to display mapped RNA seq data in gBrowse. Currently I have the data in SAM format. Maybe I can figure out a trick using the text manipulation tools. thx, Felix

Re: [galaxy-user] SAM to GFF ?

biopyt...@maubp.freeserve.co.uk Subject: Re: [galaxy-user] SAM to GFF ? To: Felix Hammer hamm...@cip.ifi.lmu.de Cc: galaxy-user@lists.bx.psu.edu Date: Friday, February 18, 2011, 8:09 AM On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote: Hi Peter, thx for the reply