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

Re: [galaxy-user] Ngs Mapping using LASTZ
by Thomas Jenner Pulikotial Augustine 29 Jul '11

29 Jul '11

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

2 1

renaming dataset in workflow
by Belinda M. Giardine 29 Jul '11

29 Jul '11

Is it possible when renaming a dataset in a workflow to have it fill in the dataset number like the default labels? For example the default label may be "Filter on data 17". What if I want it to be "High coverage on data 17"? Could I put some special variable in the text to tell Galaxy to fill in the data number? If it isn't possible please consider this as a feature request. Thanks, Belinda

2 1

blastn Q.
by Todd Yilk 28 Jul '11

28 Jul '11

Hello all, I'm using the blastn tool and Galaxy is generating this command (pasting from the log file): command is: perl /opt/galaxy/dev/galaxy_dist_dev_umma/tools/blast/psub -l galaxy_normal.c --fasta /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1377.dat --cat /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1378.dat blastn -query "/opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1377.dat" -db "/house/blast_db/ncbi/nt/2011-01-11/nt" -task blastn -evalue 0.001 -out /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1378.dat -outfmt "6" It's failing in Galaxy and I get a "script psub: No such file" kind of error running it at the command line ... I'm assuming psub here isn't the Unix command. According to find, my Galaxy installation doesn't have a galaxy_normal.c file either. Is there something I didn't install? Thanks, - Todd Yilk Software Developer Los Alamos National Laboratory

2 2

Galaxy News Page and RSS Feed
by Dave Clements 28 Jul '11

28 Jul '11

Hello all, The new Galaxy wiki features a Galaxy News page and RSS feed for items of interest to the Galaxy community. The news page is a good way to get information out to the community and is less intrusive than posting to the Galaxy mailing lists. Anyone can create a news items by following directions on the news page, or by sending the item to outreach(a)galaxyproject.org. News items automatically become items in the Galaxy News RSS feed, and are also automatically listed in the right bar on the wiki home page. The most recent posting is about the new Galaxy paper "Making whole genome multiple alignments usable for biologists" appearing in Bioinformatics. News Page http://wiki.g2.bx.psu.edu/News RSS Feed http://feed43.com/galaxynews.xml How to post a news item http://wiki.g2.bx.psu.edu/News#Add_a_News_Item Please let me know if you have any questions (or news items). Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

1 0

query
by archana bhardwaj 28 Jul '11

28 Jul '11

Respected sir I am using fastaq to convert fasta and quality file. But after sometime i am getting an error and m not able to fix it. please guide me what sholud i do??

3 2

symbolic link to bowtie
by Luciano Cosme 28 Jul '11

28 Jul '11

Hi, I am running Galaxy locally (Ubuntu 11.04) and I am getting this error message when I try to use mapping with bowtie: Error indexing reference sequence /bin/sh: bowtie-build: not found Then I downloaded bowtie and tried to create a symbolic link using at /bin: ln -s /home/koala2/bowtie bowtie Then I get this error message: ln: creating symbolic link `bowtie': Permission denied I know that is more a linux issue than Galaxy, but does anyone have any suggestion? I changed the permission of bowtie folder and file but keep getting same error. I am logged as administrator too. Thank you. Luciano

2 1

Re: [galaxy-user] regarding 454 chip data
by Jennifer Jackson 27 Jul '11

27 Jul '11

Hello Archana, Specific tutorial and screencast help is located here: http://main.g2.bx.psu.edu/u/james/p/exercises http://usegalaxy.org center pane, scroll to quickie #15 and click Please send all future questions directly to the mailing list and not to individual team members. galaxy-user(a)bx.psu.edu is the correct list to use for this type of question. Best wishes, Jen Galaxy team On 7/27/11 3:51 AM, archana bhardwaj wrote: > > Respected sir > > I am working on 454 chip sequence data.I want to know workflow for this > analysis . > Please guide me.. -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

1 0

BAM files loading and mandatory grooming
by Louise-Amélie Schmitt 27 Jul '11

27 Jul '11

Hello everyone Whenever we try to load BAM files without copying them, we get an error stating the files need grooming, and can't use them at all. Is it this serious? Would there be a way to bypass that? Thanks! L-A

4 8

regarding galaxy server problem
by archana bhardwaj 25 Jul '11

25 Jul '11

Respected sir There is problem in galaxy during file uploading.from 2 days i am trying to upload file..still its under processing. my file is not that much big.. if there is any problem , chk the server else..please guide me some other way of uploading .. Thank you yours obediently Archana

2 1

Re: [galaxy-user] promoter question
by Jennifer Jackson 25 Jul '11

25 Jul '11

Hello Rami, The tool "Operate on Genomic Intervals -> Get flanks" will return reference genomic sequence upstream/downstream from a set of coordinates, which is essentially what the UCSC Genome Browser is doing when you use the export promoters option. This tool requires that you already have a set of genomic intervals (a data track) from an annotation data source. UCSC is only one choice. Please see all directly linked data sources listed under "Get Data". Or, locate your own and load via URL (http/ftp) or a file that you have already downloaded to your computer/server (use ftp if large). Please note that this tool will function with most (but not all) genomes already part of the native reference genome set in Galaxy and must be assigned. To assign, use the "Edit Attributes" form by clicking on the pencil icon for the dataset. Best! Jen On 7/25/11 11:55 AM, Rami Al-Ouran wrote: > Thank you very much for the quick response. > > Does that mean there is no direct method in Galaxy (without using UCSC) > to get promoters from a list of gene symbols ? > > Thank you, > Rami > > On 7/25/2011 2:51 PM, Jennifer Jackson wrote: >> Hello Rami, >> >> The UCSC genome browser will result in one promoter sequence per >> transcript, as many genes will have many associated transcripts. >> >> Depending on which track you are obtaining data from, a "representative" >> transcript for each gene may or may not be notated. If using "UCSC >> Genes", the tables associated with the primary table knownGenes to >> examine are knownIsoforms and knownCanonical, which will show how >> transcripts are clustered. You can link these tables together using the >> output option "selected fields from primary and related tables". >> >> Alternatively, you may already have already selected a set of >> transcripts (not genes) to obtain data from. In that case, enter the >> identifiers directly into the UCSC Table browser's "identifiers" field >> when performing the query (paste or upload text file). Or pull all into >> Galaxy and join with your identifier list to subset the results. >> Identifiers must be in the same format as used by the track of interest >> for this method to work. >> >> If you are having trouble with the Table browser, the UCSC Genome team >> can help through their mailing list at http://genome.ucsc.edu >> >> Hopefully this helps to explain the data, >> >> Best, >> >> Jen >> Galaxy team >> >> On 7/25/11 10:25 AM, Rami Al-Ouran wrote: >>> Hello, >>> >>> Is there a way in galaxy to retrieve the promoter sequences for a list >>> of genes. I tried using UCSC genome browser, but in many cases it keeps >>> giving more than one promoter sequence per gene. >>> >>> Thank you, >>> Rami >>> ___________________________________________________________ >>> 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/

1 0