October 2011 - galaxy-user - lists.galaxyproject.org

GATK
by Muehlschlegel, Jochen D.,M.D. 27 Oct '11

27 Oct '11

Hi, Do you host GATK on the Galaxy server? If not, is there a way to call SNPs from NGS (RNA-seq) data using Galaxy ? Thanks Danny The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Map with Bowtie for Illumina (version 1.1.2)
by KNIGHT M.R. 27 Oct '11

27 Oct '11

Hi, I'm trying to assemble Illumina paired sequence which is at least 15x deep to the Arabidopsis genome (TAIR 10 version) using Map with Bowtie for Illumina (version 1.1.2) but try as I might with changing all the parameters in different ways to reduce stringency I am still getting a lot of gaps in the assembly (probably about 10% missing). What settings would you advise I focus on to try and improve the situation? Many thanks in advance! Marc. *** Professor Marc R. Knight, Director, Durham Centre for Crop Improvement Technology, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE. Tel: +44 191 33 41224 Fax: +44 191 33 41201 Website: http://www.dur.ac.uk/dccit/ ***

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how to merge multiple fastq files
by Jennifer Jackson 27 Oct '11

27 Oct '11

Hi Tracy, The tool "Text Manipulation -> Concatenate datasets tail-to-head" can put the two together. Then set the datatype to fastq, if needed (click on the "pencil" icon for the full dataset to reach the "Edit Attributes" form to make the change). Be sure to watch out for an extra newline being added between the two files. You can test for/eliminate this using "Filter and Sort -> Select" with the options "that: NOT Matching" and "the pattern: ^$". (the regular expression '^$' [no quotes] matches empty lines). I am sending to the galaxy-user mailing list for our internal tracking and for other users to learn from. Please send all questions directly to the list going forward, it is very helpful for us. Thanks for using Galaxy! Jen Galaxy team On 10/27/11 11:58 AM, Qingquan Liu wrote: > Hi Jennifer, > > I have sequenced one sample on 2 lanes of GAII, and now I am trying to > merge the 2 fastq files. How should I do it on Galaxy? Thank you very much! > > Best, > > Tracy > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Local instance data upload
by Luciano Cosme 27 Oct '11

27 Oct '11

Hi, I am trying to set up a ftp server to upload data in my local instance of galaxy but I am having some problems with postgres. I spent a lot of time on it already and could not solve it yet (well I am a biologist). It seems pretty straight forward process at http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP , but I it is just not working. I am running it on Ubuntu 11.10, I have a ftp server set up already, but I can't fix the postgres. Is there any other way to upload data to the local instance without using a ftp server? Well I have all files in same computer where I have galaxy, using a ftp server seems to be a extra step. The only other way that I thought was to upload the compressed files, but I have around 15 files for every sample (14 sample total) and I would have to concatenate them later on. Thank you. Luciano Cosme

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Problem with bam and/or bai files
by Mike Dufault 27 Oct '11

27 Oct '11

Hello Galaxy Team, I have been using Galaxy for SNP detection for with great success. Basically, I followed the screen-cast from Anton without any problems. The only change was to use the BWA instead of Bowtie. Until now, I have always assigned my raw read files to the hg19 format. Now I want to try the GATK pipeline to analyze my samples but I am running into a problem with the bam/bai files. Here is what I did. I imported my Illumina paired end reads into Galaxy and assigned them to the hg_g1k_v37 format instead of the Hg19 format. From there, I again followed the exact same process: FastQ Groomer, Summary Statistics, Boxplots, Align with BWA, filter on SAM, SAM-to-Bam, generate bai file. I made sure that hg_g1k_37 was chosen for the format for all of these steps that required that information. Everything seemed to run successfully as all of the boxed turned green. When I tried to view the bam file in IGV (as a QC step before the GATK pipeline), I received the following error: "Error reading bam file. This usually indicates a problem with the index (bai) file. ArrayIndexOutofBoundsException: 4682 (4682)." I did the exact same analysis using the Hg19 format and my bam/bai files worked perfectly fine in the IGV viewer. Can anyone tell me what the problem is and how to fix it? Thanks, Mike Dufault

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Map with Bowtie for Illumina (version 1.1.2)
by KNIGHT M.R. 27 Oct '11

27 Oct '11

Hi, is it possible to run Map with Bowtie for Illumina (version 1.1.2) in -v alignment mode/ If so, what settings do I need to enter? Many thanks, Marc. *** Professor Marc R. Knight, Director, Durham Centre for Crop Improvement Technology, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE. Tel: +44 191 33 41224 Fax: +44 191 33 41201 Website: http://www.dur.ac.uk/dccit/ ***

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cluster install
by Joshua Udall 26 Oct '11

26 Oct '11

Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are limited users on a local machine or on a cluster where galaxy is the main use of the cluster (so it handles all the user accounts). Where would I direct our IT admin group to get more assistance with customizing the authentication process with our existing, function cluster? -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307<tel:801-422-9307> Fax: 801-422-0008<tel:801-422-0008> USA

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Over disk quota
by GANDRILLON OLIVIER 26 Oct '11

26 Oct '11

Hello I just received the following message while using Galaxy through the web "You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota." I deleted a couple of files but it didn't helped. I checked the FAQ and could not get the answer. Thank's for your help Olivier

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sample for video for example 3 in ngs analyses in galaxy
by Linda McMahan 26 Oct '11

26 Oct '11

Hi, I am watching the video 'Example 3<http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html> - mapping paired-end Illumina run and visualizing results at UCSC Browser', and would like to try out the exercise. I don't have paired-end Illumina fastq sample, Could you provide me the sample mentioned in the video or point me to the location where I can get a small human paired-end Illumina fastq sample to try out the exercise in example 3. Thanks, Linda McMahan

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Names for genes in RNA-Seq analysis
by GANDRILLON OLIVIER 26 Oct '11

26 Oct '11

Hello I am using Galaxy to analyse RNA-seq libraries made from chicken cells. I just groomed my sequences, passed them through TopHat and then Cufflinks. This worked well and in the end I get a list of genes and their respective FPKM values. My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc… Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer). Sincerely Olivier ----- New mail adress: olivier.gandrillon(a)univ-lyon1.fr Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html "Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux" Tobie Nathan, in "Qui a tué Arlozoroff"

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