On Wed, Oct 17, 2012 at 1:30 PM, Andreas Kuntzagk
<andreas.kuntz...@mdc-berlin.de> wrote:
> In the main toolshed I find bam_to_bigwig 2 times.
> Description, Version and Requirements seem the same.
> How am I to decide which one to use?
> regards, Andreas

A little history:

Brad's was first, using pysam and wigToBigWig, and could be run
on a standalone BAM file, but initially didn't allow ignoring of
CIGAR N operations.

Lance wrote an alternative using using genomeCoverageBed and
bedGraphToBigWig allowing gaps/skips to be excluded from the
coverage calculation, which is important for RNA-Seq. However,
it did not work on standalone BAM files (e.g. reads mapped to an
in house assembly), only those with a genome defined in Galaxy.

I helped combine them to produce the updated version of Brad's tool,
which works on standalone BAM files, and can ignore CIGAR gaps/
skips. So personally we the latest version under 'brad-chapman'.

For more details, see this thread (and follow ups later in the year).

(Brad and Lance - please correct me if I've misrepresented
anything in that summary)

As this point it might be nice to make the gap/skip handling an
option in Brad's wrapper (defaulting to on to match the current


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