April 2012 - galaxy-user - lists.galaxyproject.org

Help!! Tophat paired end reads
by 杨继文 17 Apr '12

17 Apr '12

Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience?? Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ? Looking forward to your reply Jiwen

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Can we change - bwasw command in Galaxy
by shamsher jagat 17 Apr '12

17 Apr '12

I am doing alignments of 454 reads in bwa and was wondering if there is an option to change it to bwasw and use Galaxy web version? Thanks

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How to use collapsed sequence files in mapping and displaying
by Jun Lu 17 Apr '12

17 Apr '12

I found that there is a "collapse" tool under FASTA manipulation, which will significantly shorten mapping time with bowtie with small RNA reads that tend to have many reads of exact length and sequence after clipping adaptors. The tool generates new names for each unique sequence read with a number indicating the number of times (or occurrences) the unique sequence has appeared in the data. The question is, after mapping with Bowtie, how can I regain this "occurrence" information when displaying in Genome Browser? The current setting will only show one mapped read for each unique sequence, no matter how many times this unique sequence has occurred. Should I write a custom code to expand the resulting sam file based on the occurrences? All runs were executed on the galaxy main server. Any suggestion is appreciated. Jun

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Re: [galaxy-user] wig to bigwig error
by Michael Sikes 16 Apr '12

16 Apr '12

Jen, A couple of uninformed questions. I gather from your response that the author lab submitted a multiple track group .wig file instead of a single track group .wig file, and that I need to generate a single track group file before the bigwig conversion will work. So, with regard to the instructions below, I am to run the text manipulation on the original author submitted .wig file. Then run "filter and sort-- Select lines that match an expression" on the newly created file that: "Matching" the pattern: "track". This generates yet another file that has the following info: 88: Select on data 87 1 line, 1 comments format: wig, database: mm8 Info: Matching pattern: track track type=wiggle_0 visibility=full name="Smc3_mES" autoScale=on color=100,0,100 1 track visibility=dense name="Smc3_mES enriched regions - 1e-09" color=100,0,100 892178 Is the number 892173 the number of track lines? If so, do I then do the "Remove beginning of a file" using 892178 on the original author .wig file? Mike > > On Apr 16, 2012, at 10:35 AM, Jennifer Jackson wrote: > >> Hi Mike, >> >> I apologize if I wasn't clear, but the 'Select' was to show you how >> to identify the multi-track group wig files. I wanted to give you a >> way to screen similar files going forward. >> >> The wig-to-bigWig program in Galaxy comes from UCSC. It >> accepts .wig files with a single track group as input: >> http://genome.ucsc.edu/goldenPath/help/bigWig.html (see step #1) >> >> The data author lab can either submit the data as single track >> group .wig files, or, if you are confident that the multiple track >> group .wig format is expected and OK from this source, split the >> file. There are no specific tools in Galaxy to do this, but >> something like this would work: >> >> - Text Manipulation -> "Add column", "1", Iterate? = yes >> - "Select", "track" >> - note the line number of track lines >> - "Remove beginning of a file", using line numbers, and the - >> original- .wig file, to break up into individual .wig files. >> >> Good luck! >> >> Jen >> Galaxy team >> >> On 4/16/12 6:57 AM, Michael Sikes wrote: >>> Jennifer, >>> >>> Thanks for your help. I ran the filter and sort tool as advised, and >>> then ran the wig to bigwig on the new history item generated by the >>> filter. This time I got a different error: >>> 84: Wig-to-bigWig on data 83 <https://main.g2.bx.psu.edu/history> >>> 0 bytes >>> An error occurred running this job:/stdin is empty of data >>> Error running wigToBigWig. >>> / >>> <https://main.g2.bx.psu.edu/dataset/errors?id=6818347><https://main.g2.bx.psu.edu/datasets/0f70746579b165e2/show_params >>> ><https://main.g2.bx.psu.edu/tool_runner/rerun?id=6818347> >>> <https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/display/?preview=True >>> ><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/edit><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/delete?show_deleted_on… >>> > >>> 83: Select on data 49 <https://main.g2.bx.psu.edu/history> >>> 1 line, 1 comments >>> format: wig, database: mm8 >>> Info: Matching pattern: track >>> <https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/display?to_ext=wig >>> ><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/ >>> show_params><https://main.g2.bx.psu.edu/tool_runner/rerun? >>> id=6818275><https://main.g2.bx.psu.edu/history> >>> <https://main.g2.bx.psu.edu/tag/retag?item_id=b4fb2e8c767b4258&item_class=Hi… >>> ><https://main.g2.bx.psu.edu/dataset/annotate?id=b4fb2e8c767b4258> >>> >>> >>> Again, I'm sure I left off something obvious. Could you tell me >>> what I >>> did wrong? >>> >>> Thanks, >>> Mike >>> >>> On Apr 13, 2012, at 1:27 PM, Jennifer Jackson wrote: >>> >>>> Hi Michael, >>>> >>>> This particular .wig file has a data format problem that is the >>>> root >>>> cause of the conversion error. Specifically, there is an extra >>>> track >>>> line in the file. This can be found using unix tools with a grep >>>> or in >>>> Galaxy with the tool "Filter and Sort -> Select" by matching the >>>> pattern "track". >>>> >>>> Ideally this would be corrected and resubmitted by the data author >>>> before use, since how/why this was inserted and what impact it has >>>> would need to be examined. >>>> >>>> Since you noticed problems with other GEO files (conversion >>>> problems), >>>> verifying the .wig format and making any necessary corrections >>>> would >>>> also be advised. >>>> >>>> Hopefully this helps! >>>> >>>> Best, >>>> >>>> Jen >>>> Galaxy team >>>> Michael Sikes, Ph.D. Associate Professor of Immunology North Carolina State University Microbiology Department 4524A Gardner Hall Campus Box 7615 Raleigh, NC 27695 Ph: 919-513-0528 Fax: 919-515-7867 email: mlsikes(a)ncsu.edu

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GCC2012 Abstract Submission Deadline is April 16, one week from today.
by Dave Clements 16 Apr '12

16 Apr '12

Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is April 16, one week from today. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, and hope to see you in Chicago, Dave C On Mon, Feb 13, 2012 at 3:27 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are now > being accepted for oral presentations at the 2012 Galaxy Community > Conference (GCC2012) <http://wiki.g2.bx.psu.edu/Events/GCC2012>. > Submissions on any topics of interest to the Galaxy community are > encouraged. Areas of interest include, but are not limited to: > > - Best practices for local Galaxy installation and management > - Integrating tools and/or data sources into the Galaxy framework > - Deploying galaxy on different infrastructures > - Compelling or novel uses of Galaxy for biomedical analysis > > See the GCC2011 program <http://wiki.g2.bx.psu.edu/Events/GCC2011> for an > idea of the breadth of topics that can be covered. Oral presentations will > be approximately 15-20 minutes long, including time for question and > answer. There will also be an opportunity for lightning talks, which will > be solicited at the meeting. The submission deadline is April 16. See the GCC2012 > Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for > more details and how to submit. > > GCC2012 <http://wiki.g2.bx.psu.edu/Events/GCC2012> will be held, July > 25-27 in Chicago, Illinois, United States. The main meeting will run for two > full days <http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>, and be > preceded by a full day of training workshops<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>. > If you are a bioinformatics tool developer, data provider, workflow > developer, power bioinformatics user, sequencing or bioinformatics core > staff, or a data and analysis archival specialist, then GCC2012 is relevant > to you. Registration will open in March. > GCC2012 is hosted by the University of Illinois at Chicago<http://uic.edu/>, > the University of Illinois at Urbana-Champaign <http://illinois.edu/>, > and the Computation Institute <http://www.ci.anl.gov/>. > > Links: > http://galaxyproject.org/GCC2012 > http://galaxyproject.org/wiki/Events/GCC2012/Abstracts > > Thanks, > > Dave Clements > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://galaxyproject.org/wiki/ > > -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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wig to bigwig error
by Michael Sikes 16 Apr '12

16 Apr '12

Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I tried to convert it to a bigwig file. The dataset came from Bing Ren's lab, and its GEO record is here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM560344 The wig file was uploaded to Galaxy Dec. 8, 2011, and I assigned mm8 rather than mm9 based on the GEO record: 49: GSM560344_03112009_313D2AAXX_B7.wi ~960,000 lines format: wig, database: mm8 Info: uploaded wig file display at UCSC main The details for this upload are as follows: Tool: Upload File Name: GSM560344_03112009_313D2AAXX_B7.wi Created: Dec 08, 2011 Filesize: 12.1 Mb Dbkey: mm8 Format: wig Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Input Parameter Value File Format auto Genome Conditional (files_metadata) 32 Inheritance Chain GSM560344_03112009_313D2AAXX_B7.wi The wig-to-bigWig conversion on data 49 (using the wig to bigwig conversion tool in the convert formats toolbox) was run on March 21, 2012 and gave the following error: 77: Wig-to-bigWig on data 49 0 bytes An error occurred running this job:line 152351 of stdin: chromosome chr13 has 120614378 bases, but item ends at 120614600 line 298005 of stdin: chromosome chr17 has 95177420 bases, but item ends at 95177625 line 325066 of stdin: chromosome chr16 has 98252459 bases, but item ends at 9825252 The details for this operation are as follows: Tool: Wig-to-bigWig Name: Wig-to-bigWig on data 49 Created: Mar 21, 2012 Filesize: 0 bytes Dbkey: mm8 Format: bigwig Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Input Parameter Value Convert 49: GSM560344_03112009_313D2AAXX_B7.wi Conditional (settings) 1 Items to bundle in r-tree 256 Data points bundled at lowest level 1024 Clip chromosome positions True Do not use compression True Inheritance Chain Wig-to-bigWig on data 49 I gather that the chromosome ends are not being snipped off, even though I toggle this option on the galaxy conversion tool. And I know it's doing something, because if I toggle that option off, I get an error that includes "broken pipe" and simply aborts. I apologize for knowing so little about the bioinformatics involved here. And I'm sure I've overlooked something that is likely obvious to others and/or failed to provide some critical bit of info in this email. But any help would be greatly appreciated. Thanks, Mike

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Toolshed initial upload errors out
by Paul-Michael Agapow 16 Apr '12

16 Apr '12

As per the title, I'm trying to setup a toolshed for our local use. After creating a repo, I try to upload the initial file only to get: TypeError: array item must be char Which seems to happen repeatedly, i.e. it's not a passing error. While I'm here, a perhaps obvious question: where or how does the main Galaxy instance get the list of toolsheds to display? The main and test sheds are hardcoded in, I guess, but how does it pick up the local - simply by virtue of the fact that it is local? p ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, 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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Editing workflows : Server error ?
by Sandrine Hughes 16 Apr '12

16 Apr '12

Dear all, I didn't use Galaxy for some weeks now. When I tried to edit some of my workflows today I received an error message "Server error" instead. Is there any problem with the workflow editor or to edit big workflows (>40 steps) recently ? It seems that I can only edit workflows with a limited number of steps. Thanks a lot, Sandrine

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FASTQ joiner fails to join PE data.
by meganathan pr 14 Apr '12

14 Apr '12

Hi, I have HiSeq2000 paired end sequence data in two separate FASTQ files. I need to filter the low quality scored sequences from my data to have a good assembly. So I decided to join the PE reads and then filter the low quality sequences in Galaxy. To do this first I groomed the data using FASTQ groomer where I kept "Sanger" as Input FASTQ quality scores type. Then I tried to join the PE sequences using FASTQ joiner. However the FASTQ joiner did not join the PE sequences but only shown the failure Info as follows *FASTQ joiner on data 8 and data 9* 0 bytes format: fastqsanger, database: ?<https://main.g2.bx.psu.edu/datasets/d08dd42f0e2ed22b/edit> Info: There were 4000000 known sequence reads not utilized. Joined 0 of 4000000 read pairs (0.00%). I am a new user and I have no idea where I am going wrong. Please suggest me how to overcome this problem. Thanks. -- ******************************************************************************************************************

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Help!! Uploading with FTP
by 杨继文 14 Apr '12

14 Apr '12

Hi, I am uploading files to Galaxy via FTP. The speed is only 30kb/sec. Is there something wrong with my operation? or is this just normal due to Galaxy's work load? Looking forward to your answers. Thanks Jiwen

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