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

SNPeff
by Andréanne Morin 06 Aug '13

06 Aug '13

Hello, I would like to use SNPeff for annotation through GATK, However when I upload my file it seems like I cannot use it for this task. My file is .txt and is in this format : Chr location ref allele alt allele 1 1234567 A T/C What am I doing wrong? Thanks, Andréanne

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Filter fastq by percentage of ambiguous (N) bases
by Anto Praveen Rajkumar Rajamani 06 Aug '13

06 Aug '13

Hello, I like to filter my fastq files (50 bp single end Illumina RNA seq reads) by a maximum threshold (10%) of ambiguous (N) bases. I can see that the "CLIP" tool removes all reads with one or more N bases. Is there a way to remove only the reads with five or more N bases using Galaxy? Thank you. Best wishes, Anto

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Re: [galaxy-user] Galaxy server down?
by Elizabeth Clare 06 Aug '13

06 Aug '13

Hi, I think Galaxy was down earlier this week - I saw several several messages when trying to access the public server, but I'm still getting no function on the public site. Are there still problems? I can load the page now, make new workflows and set tasks but no tasks have been completed in a few days. For example, I set a file to upload yesterday and it still has the blue working indication. Tasks from two days ago are grey and "waiting to run". Any ideas what has gone wrong? Beth On Fri, Aug 2, 2013 at 12:18 PM, Elizabeth Clare < elclare.evol.biology(a)gmail.com> wrote: > Hi Jen, > > I have had little response from the galaxy public server in the last two > days (I'm in England) (https://main.g2.bx.psu.edu) At the moment I > cannot load the webpage or any page associated with it. I have had messages > "Internal Server Error" then one about a brief shut down saying we should > contact an administrator if it went on for a while. It appeared to come > back early this morning but now is unresponsive again. > > I guess I'm reporting a continual error now. Has it gone down? > > Thanks, > > Beth > > -- > > > -------------------------------- > Dr. Elizabeth L. Clare > > School of Biological and Chemical Sciences > Queen Mary University of London > Mile End Road, London E1 4NS > Room 1.02, G. E. Fogg Building > e.clare(a)qmul.ac.uk > +44 (0)207 882 5687 > > http://webspace.qmul.ac.uk/eclare/ > > "If you say yes more often than you say no, you will do interesting things > in your life" > -- -------------------------------- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.clare(a)qmul.ac.uk +44 (0)207 882 5687 http://webspace.qmul.ac.uk/eclare/ "If you say yes more often than you say no, you will do interesting things in your life"

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Galaxy Log-In and DATA
by Mersee Madison-Villar 06 Aug '13

06 Aug '13

Hi... I haven't used Galaxy for a while, and forgot my password. The problem with resetting it is that the email I used is no longer active: I graduated. I need to access the files I uploaded, as its appearing that they did not collapse in the 'collapse' function properly: I have the same region of a reference genome mapping to multiple sequences with 100% ID. Can I please get access to the account? My previous email was: mersee(a)uta.edu Thank you! Mersee -- M.J. Madison-Villar, PhD Postdoctoral Fellow, Colorado State University

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question
by Larry Simpson 05 Aug '13

05 Aug '13

Hi Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq RNA reads? The "Manipulate Fastq" utility in Galaxy may have this ability but I do not know how to create a custom inquiry. Thanks in advance for any assistance. Larry

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Using local files rather than uploading?
by Joshua Orvis 05 Aug '13

05 Aug '13

For those setups where the server is running on a large, local file system, is there a method to point Galaxy at a set of files without uploading them through the web server? This both duplicates the data and (for some reason) takes a considerable amount of time to upload. Thanks - Joshua

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Rename tool output file in Galaxy
by Sachit Adhikari 05 Aug '13

05 Aug '13

Hi group, The galaxy stores the output of the job on files/043/dataset_*ID*.dat. I have two questions here.: 1) Can I find the ID of my output from the Galaxy history? I tried Edit Attributes, Annotations, tags but couldn't find it. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Thank you. Regards, Sachit

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Fwd: HCC Mutations Workflow on Local Galaxy Instance
by Moritz Juchler 05 Aug '13

05 Aug '13

Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to setup Galaxy to find SNP's in genomes from hcc patients. I have a 64-bit openSuse 11.3 server on which I installed Galaxy locally, since we have a) very large files (>30GB per patient) and b) the data is protection sensitive. I have to run this pipeline: http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2) from this paper: http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf I have in fact some data from exactly these patients, and I want to reproduce the pipeline as similar as possible. I have this so far: https://main.g2.bx.psu.edu/u/mj--/w/ngs I would be glad to even do 2-3 steps, I wont need much more for my thesis. But I find it so hard to find any information about what to do in Galaxy in practice. The first step in the workflow of the paper I included are the statistics on page 1 of the supplements, but those aren't necessary (?). So the first step I have to do after the alignment and the sam to bam conversion and the dedupe is the first step on page 2 of the supplements: "Variant calling Tumor" Which tool in Galaxy do I have to use in order to do this and the following steps? Any hints, links to papers or answers are welcome :) Best Moritz

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How to process paired reads in Galaxy
by Larry Simpson 05 Aug '13

05 Aug '13

Hi Users How do I process paired reads from an Ilumina Miseq platform? If I first use "Groomer" and then "Filter by quality", the paired reads get out of sync. I read some responses to similar questions in this Forum that the paired reads must first be "joined" before filtering and then split for mapping. There is also a "Fastq interlacer" command to join reads. However, I also read in the Forum that Galaxy requires the filtered paired reads to be of equal length. But would not the filtering process on the joined reads also modify the length of each differently? Or can the NGS: Picard command "Paired Read Mate Fixer" be used to re-synchronize the paired reads? If there is no way around the requirement for equal lengths, then I guess that it is really not possible to process paired reads in Galaxy? But I am sure it is just my stupidity. Full disclosure: Be kind, I am a novice in this field, just learning Galaxy (which by the way is a fantastic resource!). Larry Simpson UCLA

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2014 Galaxy Training Survey
by Dave Clements 05 Aug '13

05 Aug '13

Hello all, The Galaxy Project is asking for your help on how we should focus our training efforts for the coming year. If you are interested in Galaxy Training, please take a few minutes to let us know what you would like to see offered, and where you would like training to be held: http://bit.ly/gxy14training Thanks in advance for your time and input, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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