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

Re: [galaxy-user] Fwd: Cufflinks transcript-extract
by vasu punj 30 Oct '11

30 Oct '11

You should be able to do in Biomart I think fetch seq shoudl also allow you to do the same. Vasu ________________________________ Subject: Fwd: [galaxy-user] Cufflinks transcript-extract ---------- Forwarded message ----------From: dongdong zhaoweiming <zhaoweiming1983(a)yahoo.com.cn>Date: Sat, Oct 29, 2011 at 10:38 PMSubject: [galaxy-user] Cufflinks transcript-extractTo: galaxy-user(a)bx.psu.edu Hi, I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1 Cufflinks transcript 6234876 6235400 1000 + chr1 Cufflinks exon 6234876 6235060 1000 + chr1 Cufflinks exon 6235239 6235400 1000 + (2) chr1 Cufflinks transcript 6230065 6230437 1000 chr1 Cufflinks exon 6230065 6230437 1000 I want to extract transcrip sequence from the (1) and (2). But fetch sequence could only extract genomic sequence, it only fit for transcrit which had one exon,so are there any other tools to extract transcripts which had >=2 exons sequence and combine it? Thanks a lot! weimin zhao ___________________________________________________________The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serverat usegalaxy.org. Please keep all replies on the list byusing "reply all" in your mail client. For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at: http://lists.bx.psu.edu/

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Cufflinks transcript-extract
by dongdong zhaoweiming 30 Oct '11

30 Oct '11

Hi, I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1 Cufflinks transcript 6234876 6235400 1000 +chr1 Cufflinks exon 6234876 6235060 1000 +chr1 Cufflinks exon 6235239 6235400 1000 + (2)chr1 Cufflinks transcript 6230065 6230437 1000chr1 Cufflinks exon 6230065 6230437 1000 I want to extract transcrip sequence from the (1) and (2). But fetch sequence could only extractgenomic sequence, it only fit for transcrit which had one exon,so are there any other tools to extract transcripts which had >=2 exons sequence and combine it? Thanks a lot!weimin zhao

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how to transfer gene id into protein id
by Li, Jilong (MU-Student) 29 Oct '11

29 Oct '11

Hi, I have some refseq gene id, like NM_*****. How can I transfer these gene id into protein id, like NP_****? Thank you very much! Victor

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how to manage mailing list subscriptions
by Jennifer Jackson 28 Oct '11

28 Oct '11

Hello, I have removed you from galaxy-user. Instructions to manage list membership is at the bottom of this and all mailing list messages. In short, through this link: http://lists.bx.psu.edu/ Or request help from this email: galaxy-user-owner(a)lists.bx.psu.edu. Is best not to post to the mailing list for this sort of request, especially not as a reply to another thread. Thanks, Jen Galaxy team On 10/28/11 12:49 PM, Mahjoubeh Jalali wrote: > > Dear All > > How can I de-subscribe from the mailing list? > Any help would be appreciated > > Kind Regards > M. J > ___________________________________________________________ > 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 >

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Importing existing data into Galaxy
by Oren Livne 28 Oct '11

28 Oct '11

Dear All, We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them. What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other? Thanks, Oren

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RNAseq Clostridium butyricum
by Benoit HENNUY 28 Oct '11

28 Oct '11

Hi, I would like to use Galaxy with RNAseq data generated from "Clostridium butyricum" species. Please, could you include this genome in your list ? Thank you in advance Best regards Benoit HENNUY

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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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