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

get wig file after tophat
by Ying Zhang 21 Apr '11

21 Apr '11

Hi: I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out that after the tophat analysis, we can not get the wig file from it anymore which is used to be able to. Do you have any idea of how to still be able to get the wig file after tophat analysis? Thanks a lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286

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2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
by Dave Clements 11 Apr '11

11 Apr '11

Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. *Link: http://galaxy.psu.edu/gcc2011/ * *Overview *This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers. *Registration *The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. *Link: http://galaxy.psu.edu/gcc2011/Register.html ** Abstract Submission *Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. *Link: http://galaxy.psu.edu/gcc2011/Abstracts.html * *Sponsors *The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. *Links: http://www.nbic.nl/ and http://www.nsf.gov/ * We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Re: [galaxy-user] Adding the Hydra genome to Galaxy
by Jennifer Jackson 06 Apr '11

06 Apr '11

Hello Rob, We will add this to our to-do list for new genomes. Thanks for sending the Genbank information! Next time, if you could send requests to galaxy-user, that would be very helpful for the team. Best, Jen Galaxy team On 1/3/11 12:37 PM, Rob Steele wrote: > Hi Jennifer, > Would it be possible to get the Hydra genome assembly added to Galaxy? > It has been published and is available in GenBank under accession number > ABRM00000000. > > Cheers, > Rob > > Rob Steele, Ph.D. > Professor > D240 Medical Sciences I > Department of Biological Chemistry > School of Medicine > University of California, Irvine > Irvine, CA 92697-1700 > > phone: 949-824-7341 > e-mail: resteele(a)uci.edu > fax: 949-824-2688 > web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page > -- Jennifer Jackson http://usegalaxy.org

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Cleaning of fastq files
by Felix Hammer 10 Mar '11

10 Mar '11

Hi, is there a way to clean fastq files (filter Poly-A etc.) with Galaxy? Haven't found anything so far. Also if you generally know good tools plz answer. Have seen lots of stuff for fasta and qual files but not for fastq. Thx, Felix

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Problems with the Groomer
by Felix Hammer 10 Mar '11

10 Mar '11

Hi, I'm experiencing some strange problems with the fastq groomer. Trying to groom my files I get the following error: "Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in if __name__ == "__main__": main() File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 452, in __iter__ yield self.next() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 448, in next rval.assert_sequence_quality_lengths() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 142, in assert_sequence_quality_lengths assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) AssertionError: Invalid FASTQ file: quality score length (63) does not match sequence length (36)" I've double checked the file and it should be ok. Any ideas? thx, Felix

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Import data in RGenetics
by BAULANDE Sylvain 211527 Partnerchip 10 Mar '11

10 Mar '11

dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain

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Problem Adding a Custom Build in Trackster
by Liisa Koski 08 Mar '11

08 Mar '11

Hello, I am trying to 'Add a Custom Build' to my local instance of Galaxy/Trackster. There seems to be a problem when I enter the chromosome length info, both when I paste directly on the screen and when I use the upload button (for the .len file). After I press Submit I can see the Name and Key info that I specified but it always says that the 'Number of Chroms' is 0. Is there a bug or I am doing something wrong? Thanks for you help, Liisa

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Join and Sort in Galaxy
by Felix Hammer 04 Mar '11

04 Mar '11

Hello, I have some questions about the Join and Sort tools in Galaxy. How are they implemented? Just the standard unix sort and join? I have a quite large tab file (~1,5 million lines), I want to join with a somewhat smaller file (~20 000 lines). How long will this approximately take? Is there a way to view the progress? Can I gain performance if do a sort on the column I want to join? thx, Felix

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how to find out the gene_ID correspond to CUFF ID
by Ying Zhang 01 Mar '11

01 Mar '11

Dear Everyone: I have got one output file after I run Cufflink which contain gene expression information. However, I found out for each gene_ID, it has the format like, CUFF.1151175, do you have idea of how to find out the offical gene ID correspond to this CUFF ID? Thank you very much! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286

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Is there any tool in Galaxy for trimming the Barcode in 454 sequencing data? Thanks.
by Yang Liu 28 Feb '11

28 Feb '11

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