Re: [galaxy-user] SamTools Filter Pileup Only report variants? option is misleading

Hi Jesse, We agree that the original pileup tool does not have all of the functionality that one might want. The tool authors seem to also agree, and developed an upgraded version called mpileup. This has recently been wrapped and added to the Galaxy main public instance in the same 'NGS:

Re: [galaxy-user] How can I tell what programs are used by a tool?

On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F] holly.be...@nih.gov wrote: Hi all -- I'd like to know what programs are used when I run a tool on my data. Ideally I'd also like to know what parameters are passed to command line tools. The short answer is you can't, other than by

[galaxy-user] about Mapping Quality

Hi all, I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the value of some mapping quality (the 5th column) is 255. What does it mean? And I found these reads which have mapping quality 255 mapped to unique place. Thanks! Victor