galaxy-user November 2012

galaxy-user@lists.galaxyproject.org

53 participants
59 discussions

Identification of replicate outlier
by Dave Corney 11 Nov '12

11 Nov '12

Hello list, I've been analyzing an experiment with two groups each with three replicates. My workflow was TopHat (paired end) -> Cufflinks -> CuffDiff. Unfortunately, there are not many significant differences identified by CuffDiff. I am wondering whether one of my replicates might be an outlier. Does anybody have a suggestion on how to search for an outlier? The quality statistics of the unprocessed data looked equally good for all samples, so I don't think that this is a problem. Thanks, Dave

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Teaching GALAXY
by Larry Reiter 10 Nov '12

10 Nov '12

Tried to teach a class today on ChipSeq analysis, but the local Cloud install is broken and then the Penn server froze on us. Is there something I should know? LTR -- Lawrence T. Reiter, Ph.D. Associate Professor, Department of Neurology 855 Monroe Ave., Link 415 Memphis, TN 38163 901-448-2635 (Office) 901-448-7440 (FAX) 901-448-7443 (Lab) e-mail: lreiter(a)uthsc.edu Reiter Faculty Page <http://www.uthsc.edu/neuroscience/faculty/L_Reiter.php> Reiter Citation Index <http://scholar.google.com/citations?user=-kaQJ14AAAAJ&hl=en> Tooth Study <http://tinyurl.com/88f688l>

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Unresponsive
by Kit Nazor 09 Nov '12

09 Nov '12

Does anybody know why Galaxy isnt working today or when it will be back up? It has not been able to perform the simplest of functions (get refseq genes) all day. Thanks!

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(no subject)
by Vevis, Christis 09 Nov '12

09 Nov '12

Hi, I am performing online tophat on 5 different samples which I want to compare for gene expression. Is there any simple way, after the end of tophat for all of them, with which I can have an excel table with the 5 samples and their hits? Something similar to this Vevis1 Vevis2 Vevis3 Vevis4 Vevis5 uc010kuo.1 128.8503 136.60553 146.7073 91.23218 120.325 AK311687 TRA2A Homo sapiens transformer 2 alpha homolog (Drosophila) (TRA2A), mRNA. Regards Kristis Vevis, PhD Student Cell Biology UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL, UK 020 7608 4067

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tophat
by Vevis, Christis 09 Nov '12

09 Nov '12

Hi all, I am trying to perform tophat for illumina from the main server of galaxy and is in queue for 24 hours...is that normal?? Regards Kristis Vevis, PhD Student Cell Biology UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL, UK 020 7608 4067

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Account had be deleted ?
by Diam Hsu 09 Nov '12

09 Nov '12

Dear Sir or Madam, I used to use Galaxy to analyze NGS data, but these two days I could't login my Galaxy account, it also told me that my account has been marked deleted, and asked me to contact the Galaxy administrator to restore my account. Could you help me restore my accounts because I have to use Galaxy to finish my thesis. Thank you very much for your help!!! Best regards, Dima Hsu Graduate student, Graduate Institute of Biomedical Informatics Taipei Medical University, Taipei, Taiwan Email:b1984073@gmail.com

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Byte-range request problem
by Philippe Veber 09 Nov '12

09 Nov '12

Dear all, I'm currently trying to set up a Galaxy instance behind an Apache server for my lab. I strictly applied the procedure described there: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy, using a /galaxy subdirectory, stopping before the "External user authentication" paragraph (I did not configure apache to serve the static content though). Everything works fine appart from the visualisation under IGV and UCSC. On UCSC I got the infamous "Byte-Range request was ignored by server" error. I thought putting galaxy behind apache was enough to get this working, but I obviously misunderstood something. Does it ring a bell to somebody? Philippe. PS I can provide more details (versions, URLs, etc) privately if someone wants to give a hand. Thanks for any suggestion!

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new_file_path setting in universe_wsgi.ini
by greg 09 Nov '12

09 Nov '12

I see this setting in the universe_wsgi.ini file: # Temporary files are stored in this directory. new_file_path = /scratch/galaxy Is this only used by the web server or will job runners pick up this setting and use it for temp files? I'm also wondering: 1. What sort of files go here? 2. How much space does it need? Thanks, Greg

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How to show sequence length data
by Zhiqiang Shu 09 Nov '12

09 Nov '12

Hi, there I'm new to this field and have a question when using Galaxy. I have RNA sequence data. How can I plot the graph of the length of sequence with Galaxy. Thanks!

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Installing Galaxy on a Cluster - What to do about Python
by greg 07 Nov '12

07 Nov '12

So I'm installing galaxy on our SGE cluster. I'm trying for the "unified" install option. We do have Python 2.6 installed on the cluster, but I'm not allowed to install any new libraries to it. Could anyone provide me with some basic directions on how to set it up with virtualenv? I've never used it before. And I'm using contrib/galaxy.fedora-init in init.d to start and stop the service. Would I need to reference virtualenv in there? Thanks, Greg

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galaxy-user November 2012