- galaxy-user - lists.galaxyproject.org

Bowtie: Outputting unmapped reads
by Mayank Tandon 31 Jul '13

31 Jul '13

I was hoping this question had been asked, but I haven't been able to find it. I want to output the unmapped reads from bowtie as a fastq file for subsequent mapping to other genomes (i.e. the "--un <filename>" option). I know I can extract the unmapped reads by filtering on the bitwise values in the sam output and converting to fastq with the Picard tool, but I'm using colorspace data and bowtie converts them to letterspace. My understanding (coming mostly from forums and personal discussions) was that the color-to-letter conversion was somehow lossy so mapping the colorspace data directly is always preferable. So the question is: Is bowtie's '--un' option implemented in Galaxy and if so, how do I access it? Thanks in advance! Mayank Tandon

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August 2013 Galaxy Update Newsletter is out
by Dave Clements 31 Jul '13

31 Jul '13

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Cuffdiff-cummerbund with biological replicates problem
by Mike Shamblott 31 Jul '13

31 Jul '13

I'm trying to run Cuffdiff on a set of 10 human samples with biological replication then download the results for further analyses in Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get cummerbund to acknowledge replicates. I download and rename the 11 cuffdiff output files to the names expected by cummerbund. Cummerbund builds a CuffSet with no warnings and most analyses work as expected. The problem comes any time I try to see the results of replication. For example, in cummerbund, >replicates() returns an empty set and any type of plot returns an error when replicates=T is included as an argument. There is no evidence of replication data in any of the 11 cuffdiff output files. The data is presented with the group name only. From this, I conclude that the problem is with cuffdiff, since there is no replicate data for cummerbund to build into its db. I see that there are several read group files that are produced by cuffdiff but cannot be downloaded in Galaxy. Is this the problem, and if so, how can Galaxy be used to generate data with (essential) replication? Are the p and q significance values reported in the output files a result of replicate analysis? I have tried to ask this question in several different forums without success. The responses I've gotten suggest its a Galaxy issue rather than either cuffdiff or cummerbund. I'm hoping someone here can help answer my questions. Hopeful, Mike

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Galaxy Proteomics mailing list
by Ira Cooke 31 Jul '13

31 Jul '13

Dear All, The galaxy community now has a mailing list dedicated to proteomics. If you're using galaxy to do proteomics, or if you are thinking of doing so then this list if for you. In case you missed it, there is also a proteomics wiki page at http://wiki.galaxyproject.org/Proteomics To subscribe to the galaxy-proteomics list please add your email address to the list here: http://lists.bx.psu.edu/listinfo/galaxy-proteomics See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. Many thanks to Dave C. and the Galaxy team for setting this up. Thanks Ira

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how to find repeats with galaxy
by Jennifer Jackson 30 Jul '13

30 Jul '13

Irene, This UCSC track covers the entire genome for all genomes that they support. For more information about it, you may want to contact the UCSC genome browser group. http://genome.ucsc.edu Best, Jen Galaxy team Ps: please be sure to use the mailing list next time when sending in a question. Thanks! Begin forwarded message: > From: ruth casales <ibseq12(a)gmail.com> > Date: July 30, 2013, 1:15:05 AM PDT > To: Jennifer Jackson <jen(a)bx.psu.edu> > Subject: how to find repeats with galaxy > > Hi everyone, > how can use galaxy to map cgg repeats along the whole genome? i tried with gc5base but it only maps chr22 even though i selected genome > > thanks! > ibseq

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viewing data live while tool is running
by Ketan Maheshwari 30 Jul '13

30 Jul '13

Hi, I am a relatively new Galaxy user. I am wondering if there is an example of a tool which allows users to view at the stdout/err of a tool live while it is still running to get a sense of progress it is making. The tools I have had experience with so far will save the stdout/err or an elaborate report as they are running and those results would be available for users only after the tool has completed running. Admittedly I have not searched through the toolshed exhaustively. Best, -- Ketan

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HCC Mutations Workflow on Local Galaxy Instance
by Moritz Juchler 30 Jul '13

30 Jul '13

Hello, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to setup Galaxy to find SNP's in genomes from hcc patients. I have a 64-bit openSuse 11.3 server on which I installed Galaxy locally, since we have a) very large files (>30GB per patient) and b) the data is protection sensitive. I have to run this pipeline: http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2) from this paper: http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf I have some paired end data from patients, and I want to reproduce the pipeline as similar as possible. I have this so far: https://main.g2.bx.psu.edu/u/mj--/w/ngs I would be glad to even do 2-3 steps, I wont need much more for my thesis. But I find it so hard to find any information about what to do in Galaxy in practice. The first step in the workflow of the paper I included are the statistics on page 1 of the supplements, but those aren't necessary (?). So the first step I have to do after the alignment and the sam to bam conversion and the dedupe is the first step on page 2 of the supplements: "Variant calling Tumor" Which tool in Galaxy do I have to use in order to do this and the following steps? Any hints, links to papers or answers are welcome :) I asked the Galaxy Users Mailing list 1 week ago but unfortunately I didnt get any answers. Best Moritz

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Problem with SAM-to-BAM conversion
by Fabrice BESNARD 29 Jul '13

29 Jul '13

Hello, I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis briggsae. Here are the steps of my history: 1)I uploaded and groomed two .fq files corresponding to paired-end reads. In the attributes, I choose the cb4 database. 2)I mapped them using BWA (BWA Version: 0.5.9-r16 BWA run on paired-end data). However, I used the cb3 database here, since the cb4 was not available. 3)I filtered the output SAM file for mapped reads (galaxy tool version 1.0.0). cb3 is still said to be the reference database in the filtered SAM I got as output. 4) Then I tried to convert the SAM into BAM. Here it failed. When I chose the parameters of this tool, what I had for the 1st option "Choose the source for the reference list" is either: -from the history -locally cached I chose locally cached. Then, when running the tool, and I had this message error: "20: SAM-to-BAM on data 16: converted BAM error An error occurred with this dataset: Samtools Version: 0.1.18 (r982:295) No sequences are available for build (cb3), request them by reporting this error." As recommended, I report you now this error ! I found a similar problem in the Galaxy_user mailing list... But I did not get how the problem was solved ! http://user.list.galaxyproject.org/SAM-to-BAM-conversion-problem-td4135498.… I tried to change the attributes of the SAM and filtered-SAM files to cb4, but it did not work. Note also that in the error report, the version is said to be 0.1.18. But when I click on the SAM-to-BAM tool, the header of the page says: SAM-to-BAM (version 1.1.2). I don't know if this matters or not. Could you please help me fixing this issue ? Many thanks ! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

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Illumina Methylation tool in toolshed
by Sachit Adhikari 29 Jul '13

29 Jul '13

Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit

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Launching IGB from Galaxy
by Seth Stern 25 Jul '13

25 Jul '13

Hi, Ive been trying to launch the IGB viewer by clicking the Local button on the SAM-to-BAM converter (in History). (I have a local version of the viewer running on my computer.) But instead of transferring data to the viewer (what I expected to happen), it launches the web browser with this address: http://localhost:7085/UnibrowControl?version=?&feature_url_0=http://main.g2. bx.psu.edu/display_application/bbd44e69cb8906b5ec213d3ada68caac/igb_bam/Loca l/1ce2985e52430eb3/data/SAM_to_BAM_on_data_10_and_data_20__converted_BAM_bbd 44e69cb8906b5ec213d3ada68caac.bam&sym_name_0=SAM_to_BAM_on_data_10_and_data_ 20__converted_BAM&sym_method_0=http://main.g2.bx.psu.edu/display_application /bbd44e69cb8906b5ec213d3ada68caac/igb_bam/Local/1ce2985e52430eb3/data/SAM_to _BAM_on_data_10_and_data_20__converted_BAM_bbd44e69cb8906b5ec213d3ada68caac. bam&query_url=http://main.g2.bx.psu.edu/display_application/bbd44e69cb8906b5 ec213d3ada68caac/igb_bam/Local/1ce2985e52430eb3/data/SAM_to_BAM_on_data_10_a nd_data_20__converted_BAM_bbd44e69cb8906b5ec213d3ada68caac.bam&server_url=ga laxy Can anyone help me understand what is going on ? Thanks, Seth Seth Stern, Ph.D. sethster(a)comcast.net 650 996 8726 (cell)

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