On Wed, Oct 17, 2012 at 1:30 PM, Andreas Kuntzagk <andreas.kuntzagk@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). http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-April/009403.html (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 behaviour). Regards, Peter