Re: [galaxy-user] MACS on galaxy not responding

Hi Amit, The pubic Main Galaxy instance has been experiencing intermittent performance issues lately related to upgrades - we posted a yellow banner on the server yesterday to help explain. We do our best to mitigate these to reduce inconvenience but there are still delays at times. We want t

Re: [galaxy-user] macs error for chipseq data

Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/To

Re: [galaxy-user] MACS failed because of lambdaset options

Hello Philipe, Is this problem occurring on the public Main Galaxy server at http://main.g2.bx.psu (usegalaxy.org)? If so, please submit a bug report so that we can examine. http://wiki.g2.bx.psu.edu/Support#Support.Reporting_tool_errors If this is occurring on a local instance, it could be t

Re: [galaxy-user] MACS out put files from Galaxy

Hi Peter, Florian's answers are very good - I am not sure this will add much, but perhaps a little, for the Galaxy output datasets parts of the questions ... The latest Using Galaxy paper, protocol 3, includes all of the "optional" output that MACS in Galaxy will produce (in addition to the

Re: [galaxy-user] MACS out put files from Galaxy

Hi Peter, I will try to give you my basic understanding of how MACS works. But before, I would recommend you to read the MACS Readme , where you will find detailed explanations of how MACS works and what the different output files are. 1.

Re: [galaxy-user] MACS- Duplicate reads removal

Hello Yanina, According to the MACS documentation (also linked from the tool form): http://liulab.dfci.harvard.edu/MACS/00README.html The option controlling duplicates is (quote): --keep-dup=KEEPDUPLICATES It controls the MACS behavior towards duplicate tags at the exact same location --

Re: [galaxy-user] Macs

Hi Keith, To address both of your questions: Interval files with the fdr value can be created by checking the option "Parse xls files into into distinct interval files". MACS builds it model using all chromosomes, so features of one chromosome will affect the outcome from another. For spec

Re: [galaxy-user] MACS

Hello Falak, Apologies for the delay in reply. Are you still having issues? Is so, sharing a link to a history that demonstrates the issue would be helpful. You can email the link directly to me if you need to keep your data private. Best, Jen Galaxy team On 4/7/11 9:00 AM, Sher, Falak wro

Re: [galaxy-user] MACS follow up

Hi Keith, This does sound like a BED file format issue if that is your input type. A BED6 is necessary to capture strand. BED is different from Interval in that all columns are required to be in a specific order. In addition, all prior columns are required for later columns to be identified c