[galaxy-user] Xgrid and Galaxy
Hello, I'm trying to determine if Galaxy will work with Xgrid to set up a small cluster of Mac's for next-gen sequencing projects. I saw on http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server that Galaxy supports Torque PBS or Sun Grid. I don't think that Sun Grid runs on Snow Leopard and I don't know about Torque. Snow Leopard already comes with Xgrid so I was hoping to use it. Thank you for your help, Paul Cantalupo University of Pittsburgh ___ 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] question about the GATK tools
Hi, I just uploaded the BAM file for an exome sequencing sample and was trying to use the GATK tools. In the first step, realigner Target creator, I can see my uploaded file but I can't see any options under the using reference genome and the following choices so I can't click execute. Did I do anything wrong? Thanks! Xiaojing Hong University of Iowa ___ 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] Cufflinks with reference annotation and without reference annotation
Crystal, If you provide a gene annotation to Cufflinks, the transcripts produced will match those in the annotation exactly. If you assemble without a gene annotation, the transcripts produced will match the reference in some cases, but, in others, will not match the reference due to small and/or large errors. Because '=' denotes an exact match between an assembled transcript and a reference transcript, more '=' are to be expected when Cufflinks has a gene annotation. Finally, a couple procedural issues: *please send questions about analyses and tool usage to the galaxy- user mailing list, not galaxy-dev or individual developers; *please do not send duplicate emails as it can confuse our tracking system and slow down our response rather than speed it up. Good luck, J. On Aug 17, 2011, at 9:14 AM, Crystal Goh wrote: Hi, I am Crystal. I have some problem with Cuffdiff output. Hope can get some advice. Thanks. After aligning RNA-seq reads with Tophat, I used the Tophat output for Cufflinks. For Cufflinks, I tried two approaches and compared the results: 1st approach: Put zebrafish Ensembl GTF as reference annotation 2nd approach: without reference annotation. From the output of above 2 approaches, I continued with Cuffcompare (with reference annotation) and Cuffdiff, Attached word document is the workflow and parameters I set for these 2 approaches. When I compared the output of Cuffdiff between these 2 approaches, a total of 48584 tracking id with class code = was observed in trancript FPKM tracking file from Approach 1, whereas there is only 1248 tracking id with class code '=' from Approach 2 (I attached transcript FPKM tracking files from approach 1 and 2) In my opinion, I should observe 48584 tracking id with class code '=' and additional tracking id with other class codes in transcript FPKM tracking file from Approach 2. Can I get advice on this? Thank you. Best regards, Crystal Workflow and parameter for 2 approaches.zipApproach 1 Transcript FPKM tracking (Cufflinks with reference annotation).zipApproach 2 Transcript FPKM tracking (Cufflinks without reference annotation).zip ___ 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] file size limit/authorization
Is there a specific limit to the size of files that one can upload to Galaxy? I have a couple of 7 Gb files that I'm considering uploading (by ftp as suggested), but I don't want to be a storage hog. Do I need any authorization other than the account that I've registered for? Thanks, David B. ___ 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] visualization of alignment
Hello Tao, For the Bowtie results, the aligned results may be low because the data is RNA and not DNA. TopHat is generally considered a better choice for RNA since it allows for bridges over splice sites (introns). The full documentation for each program is on each tool's form and/or you can contact the tool authors with scientific questions at tophat.cuffli...@gmail.com. Also, a tutorial and FAQ are available here: http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq For visualization, an update that allows the use of a user-specified fasta reference genome is coming out very soon. For now, you can view annotation by creating a custom genome build, but the actual reference will be not included. Use Visualization - New Track Browser and follow the instructions for Is the build not listed here? Add a Custom Build. Help for using the tool is available here: http://galaxyproject.org/Learn/Visualization As stated before, please email the mailing list directly and not individual team members. Specifically, with a to to the mailing list (only) and not including team members as a to or cc unless ask to do so when sharing private data. Our internal tracking system and public archives rely on this method. Thank you for your future corporation. Best, Jen Galaxy team On 8/18/11 3:15 PM, Peng, Tao wrote: Hi jen, I have used BOWTIE to align my RNA-seq reads to HSV2 genome; out of 35,000,000 lines, only 621 lines left when I chose to have mapped reads only. How can visualize these aligned reads to HSV-2 genome? In the panel of converted SAM to BAM, I tried to use the data in trickster, but I am not sure to how to build a HSV genome as a reference? I appreciate your help, tao -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
