28 Mar
2011
28 Mar
'11
4:41 p.m.
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