On Mon, Mar 28, 2011 at 3:11 PM, Sher, Falak wrote: > My second question is, > 2) How can I convert SAM/BAM formated files (generated by Bowtie > mapping tool at Galaxy) to Wiggle or Bigwig formats.
Brad Chapman has written a Galaxy tool for converting BAM to BigWig, called "Calculates coverage from a BAM alignment file". This is available from the Galaxy Tool Shed http://community.g2.bx.psu.edu/ if you have your own local install of Galaxy. It uses a Python script (which can be run easily outside Galaxy) which converts from BAM to Wiggle, and then calls the wigToBigWig tool from UCSC to convert this to a BigWig file. Peter ___________________________________________________________ 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/