- galaxy-user - lists.galaxyproject.org

Operate on genomic intervals
by Sarah 28 Oct '11

28 Oct '11

Hi All, I have two files containing multiple scaffolds and their genomic intervals. Now I want to substract the intervals of one file from the other, but apparently this tool is only available if all the data in the chromosome column have the same name. Does anybody known a way how to handle files with different names in the chromosome column? Thanks a lot in advance, Sarah

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Re: [galaxy-user] GATK
by Jennifer Jackson 28 Oct '11

28 Oct '11

Hi Danny, On 10/28/11 8:53 AM, Muehlschlegel, Jochen D.,M.D. wrote: > Hi Jen, > > Great. I am uploading data right now and will try it. It would be a great > addition if it worked and I will give you feedback. > > On another note, is Galaxy in the meantime able to do a cufflinks, > specifically Cuffdiff analysis, on paired-end data ? Yes, this options is included on the CuffDiff tool form as an option. Paired vs mate paired data questions would be best directed to the tool authors at tophat.cufflinks(a)gmail.com. Best, Jen Galaxy team > Thanks > > Danny > > > > > > > On 10/27/11 4:56 PM, "Jennifer Jackson"<jen(a)bx.psu.edu> wrote: > >> Hi Danny, >> >> A beta GATK pipeline is available on our Test instance at: >> http://test.g2.bx.psu.edu/ >> >> Feedback about the tool suite is welcomed! >> >> Best, >> >> Jen >> Galaxy team >> >> On 10/27/11 1:08 PM, Muehlschlegel, Jochen D.,M.D. wrote: >>> 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. >>> >>> >>> ___________________________________________________________ >>> 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://usegalaxy.org >> http://galaxyproject.org/wiki/Support > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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how to merge multiple fastq files
by Jennifer Jackson 28 Oct '11

28 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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how to merge multiple files
by Jennifer Jackson 28 Oct '11

28 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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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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