[galaxy-user] Tophat

Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance.

Re: [galaxy-user] Fwd: visualisation of a bam file

Hello, I was able to create a visualization using hg19 as the reference and load this dataset and visualize it. It is important to allow the BAM file to index fully, do not navigate away from the page while this is going on. As a test, I also used SAMTools BAM-to-SAM, then SAM-to-BAM (with

[galaxy-user] Dataset name in dataset file

Hi all, I have a question about a weird usage of galaxy: suppose I have 23 files, each for a chromosome, suppose the dataset name (in history) contains the chromosome name but the dataset content don't (i.e. I only have chrom position and 2 associated values), is there a way to add a column so

Re: [galaxy-user] Fwd: visualisation of a bam file

Visualization dataset index correction, please see below: On 3/7/12 6:56 AM, Jennifer Jackson wrote: Hello, I was able to create a visualization using hg19 as the reference and load this dataset and visualize it. It is important to allow the BAM file to index fully, do not navigate away from

[galaxy-user] Fwd: Question about plotting circos plot

My apology for re-posting the same question however I believe my first message was returned. I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool

Re: [galaxy-user] Question about plotting circos plot

Hi Shamsher. We have a small initial wrapper for circos. Its not complete yet and we are not sure if its even possible to wrap such a complex tool in a good galaxy UI. But if you are interested i can share our code. Cheers, Bjoern I wonder if is it possible to visualize mutation data in

Re: [galaxy-user] description of Find diagnostic hits

Hi Will, An short description of what the Metagenomics tools do is on each of the tool forms. One bit that many be confusing is that what is often called the Fetch Taxonomic Ranks tool on these forms has been renamed to be the Fetch taxonomic representation tool. In short, the Find

Re: [galaxy-user] description of Find diagnostic hits

Hi Jen, Thank you for getting back to me and for pointing out the live projects, which definitely will provide some great resources for me. Cheers, Will On Mar 7, 2012, at 5:50 PM, Jennifer Jackson wrote: Hi Will, An short description of what the Metagenomics tools do is on each of the

Re: [galaxy-user] Metagenomics

Hi Vincent, Scott, Filtering raw hits is an important part of a metagenomics analysis pipeline. Please see the methods described in the published metagenomics analysis paper associated with this tool set: Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, and

Re: [galaxy-user] FastQC in main galaxy server?

Hi Daniel, This was due to a small problem on a couple of our cluster nodes and we believe that this has been corrected. Please re-run you job and let us know if this error comes up again, Thank you for reporting the problem! Best, Jen Galaxy team On 3/6/12 11:49 AM, Daniel Sobral