Re: [galaxy-user] running cufflinks

On Tue, Sep 6, 2011 at 9:29 PM, Peng, Tao wrote: > Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY > ensemble were recognized by GALAXY cufflinks as a GTF file although they > all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as > GFF files? > > Thx, I'm pr

Re: [galaxy-user] Chip-Seq, Encode Peaks and Galaxy

Hi Rad, Jorge, Sorry for the delay in reply. We have not yet released a pre-canned workflow to do this. However, if you are looking to associate one set of Genomic interval/region data with another set, Galaxy's interval operation tools are a good place to begin. There are good examples of usi

[galaxy-user] mpileup tool

Hi all, It seems that the more recent "mpileup" tool that is a part of SAMtools offer better indel prediction than the current "pileup" tool. I've found the following thread http://gmod.827538.n3.nabble.com/samtools-mpileup-update-td3277940.html ...and the following issue https://bitbucket.org/ga

Re: [galaxy-user] mpileup tool

Hi Keith, A SAMTools update is being discussed internally. I can't comment yet about when exactly this would be implemented, but when the time comes the details would be made public in the Galaxy Announcements and News Brief: http://galaxyproject.org/wiki/News There are also a few bitbucket t