[galaxy-user] Cuffdiff errors

Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my conditions. I successfully used Cuffdiff three days ago to compare two sets of data that are processed the exact same way (align with Tophat and use Picard to confirm adequate alignment). I am using

[galaxy-user] Trackster errors

Hello I would like to visualize the tracks of my tophat accepted hits bam file. I ran my first sample that was ~10,000,000 reads and it could be visualized in both Trackster and the UCSC genome browser. When I tried to visualize my other samples (which ranged from 15,000,000 to 35,000,000 reads)

[galaxy-user] January 20, 2012 Galaxy Development News Brief

January 20, 2012 Galaxy Development News Brief Highlights: * New Object Store data integration layer introduced * RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, CuffCompare to 1.3.0. * Tool Shed installation features and community tool additions * Trackster performance upgrades and

Re: [galaxy-user] Looking for an easy load test for Galaxy Cloudman

Hi Greg, We have a tutorial workflow from one of our publications that would be a good test case to use: http://usegalaxy.org/heteroplasmy It contains complete references and the text walks through from start to end and includes expected results. The Shared Workflows area on Galaxy main

Re: [galaxy-user] Cuffdiff errors

Hello Erin, This was a temporary problem due to a new filesystem we installed during this time frame, that has since been resolved. Please try again and if the problem persists, please send a bug report from the error dataset using the green bug icon. This allows us to gain access to the

Re: [galaxy-user] Trackster errors

Erin, This was due to a temporary issue that has been fixed. However, you'll need to copy the problematic datasets and use the new copy for visualization. To copy datasets, use History Options -- Copy Datasets; you can select the source history as your target history to copy datasets within a

Re: [galaxy-user] Could you please add Vibrio cholerae O1 biovar eltor str. N16961 to the reference genome？

Hello Tao, This genome is labeled in Galaxy as: Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) However, I am guessing that the genome is not indexed for the tools you want to use it with. This means that you will need to use it as a custom reference genome. The first step is to