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

cuffmerge question
by Carol Munroe 14 Aug '11

14 Aug '11

I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find an answer in the Galaxy-user or Seq-answers archives. My question is, if I use the public Galaxy server interface to TopHat and Cufflinks, is there any access to "cuffmerge"? Also, I'm trying to understand the difference between using cuffmerge and then using cuffcompare (without a reference genome) to assemble gtf transcript files produced by Cufflinks for each group of 3 Illumina paired-end reads corresponding to biological replicates, in order to use the resulting combined gtf file for comparing the TopHat alignments of two such groups using cuffdiff. Is there any difference in the output between cuffdiff and cuffcompare, using in this fashion? For example, do they form the "union" of transcripts by the same rules, and do their outputs contain (or lack) the same columns (strand, perhaps??) I've read things on seq-answers indicating that I should be using cuffmerge, but I can't find it on the public server and apparently haven't installed it properly on my own computer so far.

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Filter out Positive Strand
by Edward Turk 13 Aug '11

13 Aug '11

Hello all, I have used Tophat to map and now I want to filter out all reads that mapped to the positive strand. Any help would be greatly appreciated. Thanks, Edward Turk

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Toronto GMOD meeting registration now open
by Dave Clements 12 Aug '11

12 Aug '11

Hello all, The next GMOD meeting has been schedule for this October in Toronto. See below for details. Dave C ---------- Forwarded message ---------- From: Scott Cain <scott(a)scottcain.net> Date: Fri, Aug 12, 2011 at 9:23 AM Subject: [Gmod-announce] Toronto GMOD meeting registration now open Hello, I am pleased to announce that registration is now open for the October 12-13 GMOD meeting at OICR in Toronto, Canada. Please visit the registration site at: http://gmod.eventbrite.com/ The registration fee for the meeting is $40 if registered before September 13. After September 13, the registration fee goes up to $50. For more information about the meeting, including information on our excellent keynote speakers, Gary Bader and Michael Brudno, please visit the meeting page: http://gmod.org/wiki/October_2011_GMOD_Meeting While at the meeting page, please make sure to suggest topics, talks and satellites for the meeting. I look forward to seeing you in Toronto! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------------------------------------------------------------------------- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Galaxy installation contractors in UK
by Paul-Michael Agapow 11 Aug '11

11 Aug '11

Perhaps a better question for the dev list but: It looks as if we are going to be getting a small lump of money to upgrade our Galaxy instance for wider use within our division. This will course mean setting up a new server and installing Galaxy, but there are some other things we'd like: adapting for use with our cluster, setting up automatic data flows into Galaxy, solid web configuration, load balancing, etc. We (the overrun core staff) haven't found the time for and probably never will. But we might be able to find the money for a contractor ... So, any pointers on finding a Galaxy installation and configuration guru in London? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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SOLID to fastq for Bowtie
by Shalabh Sharma 10 Aug '11

10 Aug '11

Hi, I am trying to implement a SOLID pipeline for my solid data. I really like the pipeline used in Galaxy, I was looking for conversion of SOLID to fastq, but it didn't say that how it is achieved in Galaxy. I know for bwa you can use solid2fasta.pl but for bowtie i did not find any program or information. I would really appreciate if you can help me with this, like how it is achieved and where i can download the program used by Galaxy. Thanks Shalabh Sharma ----------------------------- Shalabh Sharma Scientific Computing Professional Associate (Bioinformatics Specialist) Department of Marine Sciences University of Georgia Athens, GA 30602-3636

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Re: [galaxy-user] Ngs Mapping using LASTZ
by Jennifer Jackson 10 Aug '11

10 Aug '11

Hello Thomas, Using Tophat would be fine. To understand the parameters used, click on the "i" icon in the job run's dataset box in the history. For certain tools, this is also captured (line command) in the "Info:" field after the job completes. Take care, Jen Galaxy team On 8/9/11 1:28 AM, Thomas Jenner Pulikotial Augustine wrote: > Hi, > > I would like to know whether i should use Tophat or LASTZ for > transcriptome analysis, the reads(transcriptome) were obtain from 454 GS > flx sequencer. Kindly reply, in the FAQ section we're suggested to use > Tophat but this was designed for Illumina genome analyzer. Thanks in > advance. > > Br, > Thomas > > On Mon, Aug 8, 2011 at 1:40 PM, Thomas Jenner Pulikotial Augustine > <pulikotial(a)gmail.com <mailto:pulikotial@gmail.com>> wrote: > > Hi, > > I would like to know the default options used by Galaxy to align 454 > reads to reference genome using LASTZ alignment software. I'm trying > to align the query to a reference genome, kindly tell the me list of > options used for aligning the reads to reference genome. An > additional question, does Galaxy share scripts? i can across a link > that seems to be sharing scripts. > > Br, > Thomas > > > On Sat, Jul 30, 2011 at 1:44 AM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello Thomas, > > For 454 data, there is a specific screencast that may be of > interest. Go to http://usegalaxy.org and scroll in the middle > pane to find quickie #15. > > We have had very high usage over the last few days, but have > since been able to clear out more resource. Your job will likely > start within the next 24 hrs. > > Hopefully this helps, > > Thank you! > > Jen > Galaxy team > > > On 7/29/11 4:18 AM, Thomas Jenner Pulikotial Augustine wrote: > > Hi, > > I'm trying to map a data set containing 454 reads to a > reference genome > using LASTZ alignment package in Galaxy. I'm following a > workflow used > for Illumina reads with the only change in the alignment > package, i'm > using LASTZ instead of bowtie/bwa. The following is the > procedure please > correct me if it's wrong and do suggest any additional > procedure to make > the workflow better. > > In addition to this i'm, trying to do metagenomics analysis > as well > by following the procedure given in one of the video > tutorials. I've > submitted the files for alignment and its been a day since the > submission and the process has not yet started, could you > tell me what > could be the reason. The file size is 110Mb, under history > the package > indicate "Job is waiting run" how long does it usually take > to initiate > the process in the queue. Your suggestion's are valuable, > thanks for > developing Galaxy. > > Kindly help, thank you. > > 1.Uploaded a FASTA file as input > 2.Align using LASTZ > 3.Filtering SAM files on bit-wise flag values > 4.Finding how many reads are mapped to each chromosome > 5.Sort the read counts > 6.convert sam to bam > 7.perform flagstat operation > > Br, > Thomas > > > _____________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://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 > <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/__Support > <http://galaxyproject.org/Support> > > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Re: [galaxy-user] BedGraph format
by John Wu 09 Aug '11

09 Aug '11

Hi Jen, Thanks for your answer. However, when I followed your instructions, I found that the forth column in my dataset, which is the expression level (or base depth covered by short read sequences), would be treated as names instead of values. Therefore I cannot see histogram on UCSC genome browser.. Could you help me more about the question? Thanks a lot! Please see the following link to view my dataset. http://main.g2.bx.psu.edu/u/johnwu/h/human-bodymap2 John Wu -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 05, 2011 10:16 PM To: 吳正華 Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] BedGraph format Hello John, A file in bedgraph format should display at UCSC. I think that #3 (below) is your concern, but there are a few things to check if the display at UCSC link is not showing up for the dataset: 1. File is tab delimited (not space or other) and four columns, such as (from the UCSC web site's example: http://genome.ucsc.edu/goldenPath/help/bedgraph.html) chr19 59302000 59302300 -1.0 chr19 59302300 59302600 -0.75 chr19 59302600 59302900 -0.50 chr19 59302900 59303200 -0.25 chr19 59303200 59303500 0.0 chr19 59303500 59303800 0.25 2. Use "Edit Attributes" to assign a database (click on pencil icon in dataset). Confirm that this database is at UCSC by matching the database short name "dbkey" with that used in Galaxy. If the database is not at UCSC, then Visualization within Galaxy is still an option (Trackster). You can pull in other tracks from UCSC or other sources to view all of the data together for custom genomes. 3. Use "Edit Attributes" to also assign the file format as "bedgraph". The metadata will be automatically detected. The fourth column is not explicitly labeled as being a data value for display, but that does not impact display. Not all values for all datatypes are labeled the same as external sites do, yet many display correctly based on the file format type assigned. 4. Optional: create a track line using "Graph/Display Data -> Build custom track for UCSC genome browser". This is not necessary, but does allow for some user-defined labels. For full control over the track and (again, optional) browser lines used by UCSC, create this information in a text file on your computer, save, load into Galaxy, and merge with the bedgraph data using "Text Manipulation -> Concatenate datasets tail-to-head". If this does not help and you are still having issues on the public Galaxy server at http://usegalaxy.org, please send a shared history link and I can take a look and provide feedback ("Options -> Share or Publish, generate link, and email back directly to me). But, hopefully the above helps to resolve anything that was unclear. I just tested a bedgraph a few minutes ago, to confirm that there were no issue between Galaxy & UCSC for a sample bedgraph dataset, and it worked fine. Best! Jen Galaxy team On 8/4/11 9:01 PM, 吳正華 wrote: > Dear all: > > I want to transform a text file to BedGraph format and show it on UCSC > genome browser, but it seems that in galaxy I cannot assign a column > that has values in configuration screen (BedGraph format). > > How should I do the above task in galaxy? > > Thanks > > John Wu > > > > ___________________________________________________________ > 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/Support

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loading fasq.gz files using FTP
by Peng, Tao 09 Aug '11

09 Aug '11

Hi I am NEW to RNA-seq data and galaxy programs. When I try to up-load the RNA-seq data using FileZilla using my desktop PC, each file (about350 MB) takes about 1 hour to up-load. Realizing I have 4 samples, each sample has 9 fasq.gz files, each file is about 350 GB, I really need some advice how to make this up-load work. Thanks, Tao tpeng(a)fhcrc.org

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Unable to queue tophat's job for execution
by Carlos Borroto 09 Aug '11

09 Aug '11

Hi, The main Galaxy server is failing to schedule tophat's jobs. Giving error: "Unable to queue job for execution. Resubmitting the job may succeed." I've been able to run other tools jobs. Thanks, Carlos

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mi-tools- tools_fabfile.py permissions requirements (local install)
by Joseph Hargitai 09 Aug '11

09 Aug '11

Enis, a few things we came across: a, local install R - not the correct download url, rpy - will this be fixed? permissions: the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders. Is there a way to install as galaxy user only? If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder? b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?) best, joe

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