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). 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
