June 2010 - galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] [galaxy-bugs] Help with mRNA sequences
by Anton Nekrutenko 08 Jun '10

08 Jun '10

Lee-Ann: I shared a history (using chr22 data for simplicity): http://main.g2.bx.psu.edu/u/aun1/h/mrna-snps-example and a workflow: http://main.g2.bx.psu.edu/u/aun1/w/mrna-snps-example with you that do the trick. Basically, you 1. download mRNA data as BED and as mRNA sequences (history items 1 & 2) 2. Collapse sequences to tab-delimited format (history item 3) 3. Remove dots and numbers by replacing dots with tabs and cutting accession and sequence out (History items 4 & 5) 4. Join sequences with bed file (History item 6) 5. Downloading the SNPs (History item # 7) 6. Joining with SNPs (History item # 8). You can use workflow to run this analysis genomewide. Let me know if you have issues. Tx, anton galaxy team On Jun 8, 2010, at 6:56 AM, Lee Wood wrote: > Hi Anton > > Sorry to reply directly to you, but I'm a bit desperate :) . The > problem I'm having is not with joining the files. The problem is > that I need to retrieve the mRNA co-ordiantes and mRNA sequences > from Galaxy. So basically what I want is a file that contains the > mRNA co-ordinates and sequences, this file will then be joined to > the file containing SNPs to identify which SNPs are within which > mRNAs. > > The problem is that I can't retrieve the mRNA co-ordinates. When I > go through the mRNA group and track for RefSeq genes it gives me > transcript and not mRNA co-ordinates. Then I thought if I use the > refSeqAli table instead of RefSeq genes I could get the co- > ordinates, and join this file to the file containing the mRNA > sequences (that I retieved by chosing output format as sequence and > selecting sequence type as mRNA). The problem here is that because > the sequence file only contains the mRNA accession number and > sequence I have to join the two files based on the NM numbers. But > in the refSeqAli file (co-ordinates file) the NM number looks > something like this NM1234 whereas in the mRNA sequence file looks > something like this NM1234.2 so they won't join. > > Is there a way to retrieve the mRNA co-ordinates and sequences > through Galaxy, or will I have to create a script to do it myself? > > Sorry for the super confusing email, but I'd really really > appreciate any help. > > Thank-you > Lee-Ann > > On Tue, Jun 1, 2010 at 9:10 PM, Anton Nekrutenko <anton(a)bx.psu.edu> > wrote: > Lee-Ann: > > If you upload coordinates of mRNA mapping to the genome in BED > format and join it with coordinates of SNPs as shown in this movie: > > http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html > > you will be able to identify mRNA containing SNPs. > > Let me know if you still have issues. > > anton > galaxy team > > > > On May 31, 2010, at 7:16 AM, Lee Wood wrote: > > Hi > > Could you please help. I need to identify SNPs within mRNA > sequences. I have manged to retrieve all mRNA sequences using the > mRNA and EST group, Human mRNAs track and RefSeqGenes table, and > outputting in sequence format. The problem is, that to identify > which SNPs are within which mRNA sequences I need the mRNA co- > ordinates. If I leave everything the same in the table browser and > output as BED for example it gives me gene and transcript > information and not mRNA information. > > Your help will be greatly appreciated > Lee-Ann > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Re: [galaxy-user] Upload genome index to Galaxy for Bowtie alignment?
by Kelly Vincent 08 Jun '10

08 Jun '10

Hello, Unfortunately, it is not possible for you to upload the actual index files to public Galaxy (the indexes usually need to be built on the same platform that Bowtie will be running on), so the only option when the indexes aren't offered built-in is to supply the fasta. However, as James just mentioned, we can prepare the swine index files ourselves and provide them as a built-in option. It will just take a few days to get in place. Could you let me know where I can get the reference? If it's not from UCSC (our standard source), it might take longer to get it in place. Thanks, Kelly On Tue 8 Jun 2010, at 3:42 PM, Whyte, Jeffrey wrote: > Thanks so much for the rapid response, Kelly. > > Just to clarify, if I already have the genome indexed as .ebwt files > and upload these, will Galaxy still take longer? We have Bowtie on > our Linux cluster, but I like the unified features of Galaxy. I > will let you know if any issues come up. > > Greatly resource! > > Jeff > ----- > Jeffrey J. Whyte, PhD > Department of Biomedical Sciences > University of Missouri-Columbia > > On Jun 8, 2010, at 2:26 PM, Kelly Vincent wrote: > >> Jeff, >> >> Yes, you can upload your swine reference. Any reference file (in >> fasta >> format) can be uploaded through Get Data. Just be aware that using a >> reference from your history will make Bowtie take longer than with a >> built-in index every time you map reads (because it has to do the >> indexing of that file before doing the actual mapping). Let us know >> if >> you have any issues. >> >> Regards, >> Kelly >> >> >> >> On Tue 8 Jun 2010, at 3:19 PM, Whyte, Jeffrey wrote: >> >>> Hello, >>> >>> On the Galaxy web interface, the option to map sequences with Bowtie >>> for Illumina reads is listed under the Tools heading "NGS: Mapping". >>> >>> At the top of the page, it states, "Will you select a reference >>> genome from your history or use a built-in index?" >>> The options are: "Use a built-in index" or "Use one from the >>> history". >>> >>> I have a genome index (swine) that is not available on the "built- >>> in" list. Can I upload this index file to Galaxy under the Get Data >>> page and then select it under "Use one from the history"? >>> >>> The index file is 3 GB, so any advice is appreciated before I try to >>> upload it. >>> >>> Thanks in advance, >>> Jeff >>> ----- >>> Jeffrey J. Whyte, PhD >>> Department of Biomedical Sciences >>> University of Missouri-Columbia >>> >>> >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >> > >

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Upload genome index to Galaxy for Bowtie alignment?
by Whyte, Jeffrey 08 Jun '10

08 Jun '10

Hello, On the Galaxy web interface, the option to map sequences with Bowtie for Illumina reads is listed under the Tools heading "NGS: Mapping". At the top of the page, it states, "Will you select a reference genome from your history or use a built-in index?" The options are: "Use a built-in index" or "Use one from the history". I have a genome index (swine) that is not available on the "built-in" list. Can I upload this index file to Galaxy under the Get Data page and then select it under "Use one from the history"? The index file is 3 GB, so any advice is appreciated before I try to upload it. Thanks in advance, Jeff ----- Jeffrey J. Whyte, PhD Department of Biomedical Sciences University of Missouri-Columbia

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Re: [galaxy-user] Welcome to the "galaxy-user" mailing list
by Ana Sevilla 08 Jun '10

08 Jun '10

On Tue, Jun 8, 2010 at 2:59 PM, <galaxy-user-request(a)lists.bx.psu.edu>wrote: > Welcome to the galaxy-user(a)lists.bx.psu.edu mailing list! > > To post to this list, send your email to: > > galaxy-user(a)lists.bx.psu.edu > > General information about the mailing list is at: > > http://lists.bx.psu.edu/listinfo/galaxy-user > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > http://lists.bx.psu.edu/options/galaxy-user/anasevilla7%40gmail.com > > You can also make such adjustments via email by sending a message to: > > galaxy-user-request(a)lists.bx.psu.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > uxniatar > > Normally, Mailman will remind you of your lists.bx.psu.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > -- Ana Sevilla Hernandez Mount Sinai School of Medicine. 1425 Madison Ave. (Icahn Building) Floor 13. Room 26 Phone: (001) 212 659 8251 E-mail: Ana.Sevilla(a)mssm.edu

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Fwd: [galaxy-bugs] Help with mRNA sequences
by Anton Nekrutenko 08 Jun '10

08 Jun '10

Begin forwarded message: > From: Lee Wood <123456.wood(a)gmail.com> > Date: June 8, 2010 6:56:00 AM EDT > To: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: Re: [galaxy-bugs] Help with mRNA sequences > > Hi Anton > > Sorry to reply directly to you, but I'm a bit desperate :) . The > problem I'm having is not with joining the files. The problem is > that I need to retrieve the mRNA co-ordiantes and mRNA sequences > from Galaxy. So basically what I want is a file that contains the > mRNA co-ordinates and sequences, this file will then be joined to > the file containing SNPs to identify which SNPs are within which > mRNAs. > > The problem is that I can't retrieve the mRNA co-ordinates. When I > go through the mRNA group and track for RefSeq genes it gives me > transcript and not mRNA co-ordinates. Then I thought if I use the > refSeqAli table instead of RefSeq genes I could get the co- > ordinates, and join this file to the file containing the mRNA > sequences (that I retieved by chosing output format as sequence and > selecting sequence type as mRNA). The problem here is that because > the sequence file only contains the mRNA accession number and > sequence I have to join the two files based on the NM numbers. But > in the refSeqAli file (co-ordinates file) the NM number looks > something like this NM1234 whereas in the mRNA sequence file looks > something like this NM1234.2 so they won't join. > > Is there a way to retrieve the mRNA co-ordinates and sequences > through Galaxy, or will I have to create a script to do it myself? > > Sorry for the super confusing email, but I'd really really > appreciate any help. > > Thank-you > Lee-Ann > > On Tue, Jun 1, 2010 at 9:10 PM, Anton Nekrutenko <anton(a)bx.psu.edu> > wrote: > Lee-Ann: > > If you upload coordinates of mRNA mapping to the genome in BED > format and join it with coordinates of SNPs as shown in this movie: > > http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html > > you will be able to identify mRNA containing SNPs. > > Let me know if you still have issues. > > anton > galaxy team > > > > On May 31, 2010, at 7:16 AM, Lee Wood wrote: > > Hi > > Could you please help. I need to identify SNPs within mRNA > sequences. I have manged to retrieve all mRNA sequences using the > mRNA and EST group, Human mRNAs track and RefSeqGenes table, and > outputting in sequence format. The problem is, that to identify > which SNPs are within which mRNA sequences I need the mRNA co- > ordinates. If I leave everything the same in the table browser and > output as BED for example it gives me gene and transcript > information and not mRNA information. > > Your help will be greatly appreciated > Lee-Ann > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Problems saving workflow that includes 'manipulate fastq'
by Pip Griffin 08 Jun '10

08 Jun '10

I attempted to post this message to the list a week ago, but haven't had any replies, so may not have posted it properly. I am making a workflow without having actual data to test it on yet. When I include even a (seemingly simple) 'manipulate fastq' step, and save the workflow, it tries to save for many minutes, unsuccessfully, until I get sick of it and close the window. Can someone please tell me if there's something I can do about this? thanks Pip Griffin

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Lunch job as connected user
by Mariette 07 Jun '10

07 Jun '10

Hi, We have galaxy working on our cluster and we require user to be logged in using our ldap server. However jobs are owned by root when runing on the cluster as this user lunch galaxy. How can we configure galaxy, so the connected user is the user who own the runing job ? thanks for your help, Jerome

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Galaxy developer conference material?
by Erick Antezana 07 Jun '10

07 Jun '10

Hi, I was wondering whether there is (or will be) some Galaxy developer conference material that could be shared? e.g. slides, quickies (screencasts), experiences, etc? cheers, Erick

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Limiting user access
by Stewart Stevens 04 Jun '10

04 Jun '10

Hi, I'm trying to limit user access to our galaxy instance. I have in universe_wsgi.ini set the following: require_login = True allow_user_creation = False This does a lot of what we want, thanks for that. :-) Is there a way to allow users to create an account, requiring a confirmation from an administrator? (Who'd be notified of the account request.) Alternatively, is there a way to add a message, "Please contact {admin_emails} for an account." to the compulsory log-in screen that will link to admin contacts? Thanks, Stewart -- Stewart Stevens PhD Student University of Otago Department of Biochemistry Tel: +64(0)3 479 7863 Fax: +64(0)3 479 7866

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The uploaded file contains inappropriate content
by Erick Antezana 04 Jun '10

04 Jun '10

Hi, It seems there is a (serious) bug while "Adding datasets" via the "Upload directory of files" (with or without copying the data into Galaxy (3545:2590120aed68), i.e. (un)tick the 'No' box) if the files are in ZIP format. Actually the files get erased from the filesystem. In the "information" column, I get: Job error (click name for more info) Then, after clicking on the file name: Information about 2010.fastq.zip Message: Uploaded by: erick(a)mydomain.com Date uploaded: 2010-03-23 Build: ? Miscellaneous information: The uploaded file contains inappropriate content error We have no problems with adding unzipped files... thanks, Erick

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