[galaxy-user] galaxy wiki error
Hi I find an error in the galaxy wiki page. please see Admin/Datatypes/Adding Datatypes which URL is http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes datatype extension=foo type=galaxy.datatypes.tabular.Foobar display_in_upload=true/sniffer type=galaxy.datatypes.tabular.Foobar/ I guess there should be : between tbular and Foobar not . ___ 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] metagenomic workflow
Hi, I am trying to analyse my eukaryotic metagenome data using yours workflow for windshield splatter analysis. But I find several problems: 1- it is related to draw phylogeny, this tool fails always for most of my samples, reporting the error: incorrect tree structure. Tree string position 341 2- It is related with the summarize taxonomy step. I this case I obtain results but the number of counts are too high compared with the original reads. My samples are small, around 8000 reads and the counts obtained are more that 20 for some phyla. I guess this is not ok, as far as I understand from your paper than counts are equivalent to reads, am I right? 3- another strange thing is the fact that the number of sequences increase after run the step for select the high quality segments. Any reason for this??? I will really appreciate you help. Thanks in advance Asun ___ 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] All I want is a question answered please!
Hi Crystal, The galaxy-u...@galaxy.bx.psu.edu mailing list would be the best for this question. All lists are described here: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists http://wiki.g2.bx.psu.edu/Mailing%20Lists Grey jobs are scheduled to run the and aere in the queue. While they are waiting to run, it is important to not start and restart, as this effectively movest them to the end of the line@ Hopefully this helps, Jen Galaxy team On 7/26/12 8:57 AM, Crystal Marconett wrote: Hello, I am trying desperately to get an answer to a question. I've been over the help area for an hour trying to find an email address to ask questions to, and the only one is the tophat people's email... which is not helpful, because the problem is starting the tool in Galaxy, not getting TopHat errors yet because the job is simply stuck on grey (waiting..) The question: I am trying to start running tophat on my history in the Galaxy main wed interface. I started the job last night at 10pm. It's now 9am. The job is still waiting to run, ie. grey. How long does it take the Tophat web interface to start? is there a data limit that above which Tophat can no longer run? I don't think this is right, I've run TopHat before on Galaxy with the Illumina whole body tissue data and it took a while, but not this long My username is: cmarc...@usc.edu the History's name is: Per-RNAseq The job is : #32, 33, 34, 35 (all grey Tophat for Illumina). The history has 65.7GB in it, and says it is using 21% (I assume the amount of allocated space left on the server). Please help! And if this is not the right e-mail address can you forward this along to the correct one, please!!! or at least let me know the correct email to mail this too. Thanks! C -- Jennifer Jackson http://galaxyproject.org ___ 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] The GATK has a new website and forum
Hi everyone, Just a quick email to let you know that the GATK has a new website and forum. The new website, released in parallel with GATK version 2.0 (beta) features a much improved documentation system and user-friendly introductory materials for new users. Also, the forum is now integrated into the website and linked to the documentation, making it much easier to refer to the docs in forum discussions and find relevant information. If you hated the old Wiki, you're going to love this. http://www.broadinstitute.org/gatk/ ___ 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] cuffdiff: same gene listed with different FPKM values
Dear all, has anything like this happened to you? I compared two samples with cuffdiff and when I look at the differentially expressed genes values I have the same gene listed for 5 times with different values. E.g. sample1sample2gene 71.6837 9.76435 NM_005514 87.6456 27.3965 NM_005514 115.333 4.81687 NM_005514 38.1879 5.2753 NM_005514 69.4197 5.84387 NM_005514 112.964 3.89226 NM_005514 What does this mean? And how do I know which one represents the real expression level for that gene for the two samples? Thanks, ib ___ 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] SAM Tools Pileup
Hello Kathy, To confirm, this was run on the public Main Galaxy instance at https://main.g2.bx.psu.edu/ (usegalaxy.org ?). It could be that your intervals are overlapping with a gap region (a known gap, padded with N's - there are are several classes). This could be quickly checked by viewing the track in the UCSC Genome Browser with the Gap track set to full and the Assembly track set to dense (everything else set to hide, if you want). Zoom out as necessary. If you are still not sure, please share your history with me and I can provide feedback. Either generate a share link or add me as a share user and email me back. Use Options (gear icon) - Share or Publish. Best, Jen Galaxy team On 7/24/12 11:49 AM, So, Kathy GZ/US wrote: Hi, I’m having trouble with the Generate Pileup tool and hope that you could help me troubleshoot this. I ran the tool successfully with the following options: * Use built-in index * Print the mapping quality as the last column * Print all lines * Cap mapping quality = 60 * Call consensus = yes, then default parameters The reference bases of the entire pileup file, however, are all “N.” I double checked and the all the files have the same reference genome (mm9). Do you have any ideas on what went wrong? Thanks very much for your help, Kathy Kathy So Genzyme Corp. Functional Genomics 49 New York Ave. Framingham, MA 01701 508-271-4717 ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
