[galaxy-user] generate pileup -v

Is choosing 'Print only lines containing indels' in the 'Whether or not to print only output lines containing indels' drop down for Generate pileup, the same as the -v option in SAMTools pileup ? Matthew The information in this e-mail is intended only for the person to whom it is addressed. I

Re: [galaxy-user] cufflinks output in UCSC browser

Hello Aleks, Without seeing your history, I guess would be that you need to assign a reference genome and then confirm that that reference genome is available at UCSC. If none of this seems to be the case with your issue, please send a shared history link and we can take a look. To share a l

Re: [galaxy-user] Workflow assistance

Kevin: Yes, for Illumina data BWA would be the best option from what is currently available at the main site. You can then identify variants with pileup and compare across the samples much as it is shown at http://usegalaxy.org/heteroplasmy. This should give you a rough idea on what to expect.

Re: [galaxy-user] RNA-seq Galaxy workflow for PE barcoded samples?

Hello Jeffrey, Yes, you have this correct, please use the Barcode splitter/Splitter tool as you describe. Creating a workflow (if you haven't already) from your history after running on one dataset would be a way to simplify running the same analysis on future datasets. Apologies for the del

Re: [galaxy-user] problem in saving visualizations in trackster

Hi Suman, We have fixed this bug but it has not been pushed to our main instance yet. Sorry for the inconvenience! -K On Wed, Jul 13, 2011 at 2:39 AM, suman pal wrote: > Hello, > I am registered as jiga...@yahoo.com in Galaxy main. recently I am trying > to save visualizations in Trackster an

Re: [galaxy-user] Workflow assistance

Kevin: Is this a diploid or haploid organism? anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote: > After viewing tutorials and reading the information associated with various > tools, I ask that you point m

[galaxy-user] Workflow assistance

After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following: I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and

[galaxy-user] Galaxy Events Page and Google Calendar

Hello all, The new Galaxy wiki includes a Galaxy Eventspage ( http://wiki.g2.bx.psu.edu/Events) that lists upcoming events (such as ISMB/ECCB 2011 and the Workshop on Comparative Genomics