[galaxy-user] Xgrid and Galaxy

Hello, I'm trying to determine if Galaxy will work with Xgrid to set up a small cluster of Mac's for next-gen sequencing projects. I saw on http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server that Galaxy supports Torque PBS or Sun Grid. I don't think that Sun Grid runs on Snow

[galaxy-user] question about the GATK tools

Hi, I just uploaded the BAM file for an exome sequencing sample and was trying to use the GATK tools. In the first step, realigner Target creator, I can see my uploaded file but I can't see any options under the using reference genome and the following choices so I can't click execute. Did I

Re: [galaxy-user] Cufflinks with reference annotation and without reference annotation

Crystal, If you provide a gene annotation to Cufflinks, the transcripts produced will match those in the annotation exactly. If you assemble without a gene annotation, the transcripts produced will match the reference in some cases, but, in others, will not match the reference due to

[galaxy-user] file size limit/authorization

Is there a specific limit to the size of files that one can upload to Galaxy? I have a couple of 7 Gb files that I'm considering uploading (by ftp as suggested), but I don't want to be a storage hog. Do I need any authorization other than the account that I've registered for? Thanks, David

[galaxy-user] visualization of alignment

Hello Tao, For the Bowtie results, the aligned results may be low because the data is RNA and not DNA. TopHat is generally considered a better choice for RNA since it allows for bridges over splice sites (introns). The full documentation for each program is on each tool's form and/or you can