[galaxy-user] Error aligning sequence
Hi, I was wondering if you could help me to understand an error which I get when mapping using Galaxy: An error occurred running this job: Error aligning sequence. Warning: Exhausted best-first chunk memory for read BIO-SEQUENCER1_0011:1:1:9519:2064#CGATGT/1 (patid 703); skipping read Warning: Exhausted best-first chunk memory for read BIO-SEQUENCER1_0011:1:1:1795:6806#CGATGT/1 (patid 4461); If you know what's the error may mean, could you please let me know? Best Wishes, Agnieszka -- A Bierzynska Academic Renal Unit University of Bristol bi...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Fwd: deleting datasets from history
? : deleting datasets from history : Tue, 5 Jul 2011 19:58:45 +0300 ??: Sergei Ryazansky s.ryazan...@gmail.com : galaxy-user-requ...@lists.bx.psu.edu Hello all, After the deleating datasets from the history panel in our Galaxy mirror the indicator at the top right corner shows the same amount of used space as before deleting. Also, the files corresponded to the datasets remains in the Galaxy database/files/000 directory. It seems, that deleting of datasets from history is only delete the launch to file but not the file itself. How to configure the Galaxy mirror to delete not only records in history panel but also the corresponed files? Thank you in advance! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] problem with displaying tracks from Galaxy
Hello all, we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the redirected to non-http(s): /root error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Questions on CuffDiff Output and Browser Visualization
Kurinji, 1. when I look at my differentially expressed transcripts file (generated using ensembl hg19 as a reference with chr added on to obtain results with ensembl gene names) and search for specific genes that I am interested in I can not find them in my cuffdiff output file - even though I can visualize these genes on IGV and they look obviously differentially regulated. Also, given that the cuffdifff output for differentially expressed transcripts does list all trascripts, including the ones that have not significantly changed, wouldn't transcripts for these genes be listed anyway, even if my visual ballparking on differential regulation is not statistically significant? I would really like to know why I am missing genes from my cuffdiff output. It's not possible to answer this question in general because it's specific to your analysis; in particular, your use of a reference annotation file is going to influence Cuffdiff's outputs. You might try using positional information rather than gene names when searching through Cuffdiff files as the gene short name/ID is only used for known transcripts/genes. More detailed questions are probably best directed to the Cufflinks authors: tophat.cuffli...@gmail.com 2. do you all get a good correlation between the top differentially expressed transcripts/genes generated from cuffdiff and how the data looks when visualized on IGV - ie. do your upregulated transcripts really look upregulated when visualizing? I found that while some validate visually, some do not which is confusing Cufflinks uses multiple statistical techniques to estimate FPKM and differential expression; in some cases, it may not be possible to visually observe differential expression amongst transcripts. Alternatively, setting additional parameters (e.g. normalization) may lead to results that match what you're looking for (visually or otherwise). 3. when visualizing on a browser, and if different transcripts for one gene are regulated differently - ie. some are up in your treated sample but some are done for the same gene - how can you tell which transcriptID from cuffdiff corresponds with what you are seeing? This information can be found in Cuffdiff's transcript FPKM tracking and differential expression testing files. Good luck, J. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Looking for new transcripts with cufflinks
Will submit to Galaxy my additions. Thanks Vasu --- On Wed, 7/6/11, Jeremy Goecks jeremy.goe...@emory.edu wrote: From: Jeremy Goecks jeremy.goe...@emory.edu Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks To: vasu punj pu...@yahoo.com Cc: GavinOliver gavin.oli...@almacgroup.com, David Matthews d.a.matth...@bristol.ac.uk, galaxy-user galaxy-user@lists.bx.psu.edu Date: Wednesday, July 6, 2011, 10:08 AM One question related to this If I am intrested in annotated genes/transcripts, what change I may have to make in command line while runnig Cufflinks so that it will give both unknown as well as known transcrpts and genes? Thanks You probably want the -g/--GTF-guide parameter; from the Cufflinks documentation: -- Tells Cufflinks to use the supplied reference annotation (GFF) to guide RABT assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled. -- This isn't currently implemented in Galaxy's Cufflinks but probably will be in the future. As always, community contributions are most welcome; if you've implemented something in your Cufflinks/compare/diff Galaxy wrappers that isn't available in the Galaxy repository, please submit them to the Community site: http://community.g2.bx.psu.edu/ or send them to us. Best, J.___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Weblogo results empty
Thanks for your input and patience, Holger! Please try the new version 0.4 of the weblogo wrapper in galaxy-central #5772 - it has additional error reporting that may help clarify dependency or other problems and let me know how you go? On Tue, Jul 5, 2011 at 5:49 PM, Holger Klein h.kl...@imb-mainz.de wrote: Hi Ross, thanks for taking care of this issue. On 07/05/2011 12:31 AM, Ross wrote: Is this error seen on Galaxy main or test? If so please share the history with me so I can see the input and reproduce what sounds like a wrapper error? Otherwise, if this is on a private instance, and if the tool has never produced output successfully, then this may be a dependency installation problem - eg you may need to ensure that the weblogo3 executable is available and working correctly on the path used by your execution nodes. To assure yourself that your data works with the tool, please try running it on main using the same data, and let me know what you see? in fact it's a private instance of galaxy, it's the latest version of galaxy-dist (hg summary: 5743:720455407d1c). The input data is fine, it's a clustalw alignment in fasta format which can be used by the weblogo module on galaxy main. Maybe some background info on the weblogo installation helps: it's located below the tool_dependency_dir as defined in universe_wsgi.ini in weblogo/3.0 (with default as a link to 3.0). It contains the file env.sh which sets the PATH: export PATH=/home/galaxy/dependencies/weblogo/3.0:$PATH Starting the weblogo executable with the galaxy virtualenv python seems to work (just tested --help), although it returns a warning: ~/python/bin/python ./weblogo --help/home/galaxy/python/lib/python2.6/site-packages/CoreBio-0.5.0-py2.6.egg/corebio/seq_io/_nexus/__init__.py:19: DeprecationWarning: the sets module is deprecated import sets I also tested putting a link to the weblogo executable in the PATH that's defined for the galaxy user (as opposed to the dependency dir mechanism, that I have to admit I don't fully understand yet), but that also doesn't work. Could this be an issue of PYTHONPATH needing to be adjusted? Regards, Holger Thanks again. On Tue, Jul 5, 2011 at 12:34 AM, Holger Klein h.kl...@imb-mainz.de wrote: Dear all, I have a problem with the weblogo tool. I have a clustalw alignment in fasta format that I'd like to visualize as a logo. The sequence logo module ends with a success (green box), the info tells me the amount and length of the input data. But the output is empty, there are no plots (no matter if I select jpg, png, pdf or text). The respective image can't be displayed because it contains errors or is empty in case of text. I suspect that the actual call of the weblogo tool doesn't succeed, but I didn't figure out yet on how to check this. Does anybody have hints on where to look? Cheers, Holger ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
