January 2013 - galaxy-user - lists.galaxyproject.org

reference annotation for whole transcriptome RNA-Seq
by Davide Degli Esposti 30 Jan '13

30 Jan '13

Dear all, I am trying to get an exhaustive reference annotation for RNA-Seq analysis. I was thinking that the patched GTF annotation files for cufflinks Jeremy indicates in RNA-Seq step by step tutorial should be fine for me, but I am not able to find on the Shared data > Data libraries. Have they been replaced by iGenomes annotations? I thank you for your help Best regards Davide----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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How to run DESeq? Please Help.
by Ben Ben 28 Jan '13

28 Jan '13

Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differentially expressed transcripts from read alignments)? As far as I know, *Penn State Version* doesn't integrate the DESeq function. Thanks a lot for any response!! Best wishes, Ben

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2013 Galaxy Community Conference (GCC2013) Training Day: Please vote!
by Dave Clements 28 Jan '13

28 Jan '13

Hello all, A list of possible topics <http://bit.ly/gcc2013td> for the GCC2013 Training Day <http://bit.ly/gcc2013td> is now available at http://bit.ly/gcc2013td. Please take a few minutes to review these possibilities <http://bit.ly/gcc2013td> and *then vote for your three favorite topics* at http://bit.ly/gcc2013tdpoll* Your votes will determine not only the topics that are offered, but also which topics should be offered more than once, assigned to the larger rooms, and which ones should not be scheduled at the same time. Your vote matters. Once voting closes on 11 February, we will contact possible instructors and publish a Training Day schedule before registration opens on 22 February. *About the GCC2013 Training Day* The 2013 Galaxy Community Conference (GCC2013)<http://galaxyproject.org/GCC2013> will start on 30 June with a Training Day <http://bit.ly/gcc2013td> featuring 4 parallel tracks, each with three workshops, each of which are two hours long, for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. As always, please let us know if you have any questions. Thanks, and hope to see you in Oslo! Dave Clements, on behalf of the GCC2013 Organizing Committee * Note: You don't have to vote for exactly three topics. You can vote for fewer topics and have each vote count for more, or you can vote for more topics and have each vote count for less. Links: http://bit.ly/gcc2013td - Training Day possible topics list http://bit.ly/gcc2013tdpoll - Vote! http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Moving history datasets to libraries
by Ted Goldstein 27 Jan '13

27 Jan '13

I must be mistaken, but I don't see any way to move a dataset that I create in a history to a library except to download it and upload it again. Can this be correct? It seems like this is essential functionality. Please tell me I am wrong. Thanks, Ted

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Problem Joining Two Datasets
by Kim Spradling 25 Jan '13

25 Jan '13

Good Afternoon, I have been having problems with my Galaxy account. The upload issue I was having has been fixed, but now I can't seem to join two datasets. I have checked both text files that I want to join to ensure they have common columns, but there are no options available when I try the drop-down menu to select a sheet to join. I also get an error message stating "Either you are not allowed to view this history or the owner of this history has not made it accessible" when I first try to view one of my other saved histories, but then the files eventually appear for that saved history. Thanks, Kim

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bed file error
by ＳＣＨＥＩＮ　ＡＬＥＫＳ 24 Jan '13

24 Jan '13

Dear Galaxy users, I made a bed file from BAM for some farther analysis. Original BAM file could be nicely displayed in UCSC browser as well as in trackster. However, resulting bed file cannot be taken into UCSC-web page just stops loading without any message. Trackster returns message: "Dataset cannot be displayed due to an error" When I press "view error" button the page says "Killed". Is there any way to fix this? Best Aleks

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bwa and bowtie not working
by naveed ahmed 24 Jan '13

24 Jan '13

Dear Sir/Madam Greetings, This is to inform you that i am the user of galaxy user with an user id naveedbio(a)yahoo.com where as when i run NGS Mapping, for my sample with BWA or Bowtie illumina, it keep on job waiting for more than 24-48hrs, even though the time pass the application is not working. I tried with other samples even though the problem is persisting. Concerning this i request you to let me how to solve this problem. your return confirmation would be highly appreciable... with warm regards Naveed Ahmed Syed email: naveedbio(a)yahoo.com PReduce, Reuse, Recycle, Respect - Think before you print.

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Search software on public Galaxy servers
by Bernardo Bello 23 Jan '13

23 Jan '13

Hi community, Due to the increasing Galaxy public servers PublicGalaxyServers<http://wiki.galaxyproject.org/PublicGalaxyServers> it would be very useful to have a search tool in order to look for software ready-to-use in the public servers. Since I know this is not available. Will it be feasible? Regards, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * *

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Runtime data?
by Joshua Orvis 23 Jan '13

23 Jan '13

Maybe this is in a simple place and I'm missing it, but where can I find simple runtime data for both individual tools and larger workflow executions? I have run several different versions of a saved history using the API and want to now see how the runtimes differ between them. It can be using the interface or API, that part doesn't matter. I just don't see how to look at a saved history and get any runtime statistics. Regards - Joshua

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long waiting time for Bowtie jobs?
by Suzie Hight 23 Jan '13

23 Jan '13

Hello all, I have several Bowtie jobs that have been sitting in the queue for about 24 hours now - is there anything I may have done wrong to cause the long wait time? Thanks, Suzie Hight Suzie K. Hight, M.S. Graduate Research Assistant Minna Laboratory Hamon Center for Therapeutic Oncology 6000 Harry Hines Blvd Dallas, TX 75390 (214) 648-4909 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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