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.

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