February 2014 - galaxy-user - lists.galaxyproject.org

Converting VCF to gd_genotype
by Mike Montague 24 Feb '14

24 Feb '14

I'm interested in using the Genomic Diversity tools. I've used these with success for a previous project. For this current project, I've converted a vcf file (29 subjects) to a gd_genotype file. When I attempt to specify individuals, the checkboxes for each subject are not present. Without specifying individuals, I am unable to complete other analyses (overall FST, etc.) I cannot distinguish a difference between the vcf files that were successful from the previous project and this current project's vcf, but I assume there is a format difference that I cannot detect. I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21 22:09:49 2014 (UTC). I can share the histories of the projects if necessary. Mike -- ____________ Michael J. Montague, Ph.D. Post-Doctoral Research Associate The Genome Institute, Washington University School of Medicine 4444 Forest Park Avenue, Campus Box 8501 St. Louis, MO 63108 T. 718.809.4093 ____ This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.

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upload more than 2GB data from local computer to local installation of galaxy
by do kadya 24 Feb '14

24 Feb '14

Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says "Connection established, waiting for welcome message" and after some time

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matlab + galaxy
by do kadya 24 Feb '14

24 Feb '14

Hi, How can I call Matlab command in Galaxy ? I refer this link, but don't know how to use it. https://wiki.galaxyproject.org/HelpOnParsers?action=fullsearch&context=180&… I am learning Galaxy, hence don't know much about it. Can i write that command in xml file to integrate it as tool ? I am using below website to create xml files for Matlab. Is it good website to create xml files ? http://cli-mate.lumc.nl/define# Waiting for positive reply.

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Read simulator
by garzetti 21 Feb '14

21 Feb '14

Dear all, I would like to perforn my SNP calling pipeline (for MySeq Illumina reads) to previously sequenced and assembled genomes. Is there any read simulator in the Main Galaxy? I am looking for something like the wgsim algorithm in SAMtools... Thanks! Debora

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Re: [galaxy-user] CummeRbund - biological replicates problem
by Jennifer Jackson 20 Feb '14

20 Feb '14

Hi Tania, Yes, you are correct, the count files only address a portion of the new features. Recent updates to the underlying tools in the Tuxedo suite have resulted in issues of this sort as well (among others). The current plan is to continue with development to enhance the tool wrappers in Galaxy to support as much downstream analysis as practical. I created a new ticket as a catch-all to address this need in a global way. Details will be added as work progresses. https://trello.com/c/ugu8dty0 This is a timely and important inquiry. Our user & development community feedback is an important component in how work is prioritized. _/I encourage you and others interested in this enchantment to "up-vote" the ticket/__/in Trello./_ Comments are also welcome. Trello help: https://wiki.galaxyproject.org/Issues Best, Jen Galaxy team On 2/18/14 5:45 AM, Dottorini, Tania wrote: > Hi Jennifer, > > Thanks for your help, I did my Cuffdiff runs on 2/12/2014 but still I was not able to analyse replicates by CummerBund. The output of replicates(cuff) is empty. > > Thank you > Tania > -- Jennifer Hillman-Jackson http://galaxyproject.org

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metadata error when using megablast
by Elaine Youngman 20 Feb '14

20 Feb '14

Hello, I am attempting to megablast a FASTA file containing ~45,000 records of 100nt each against the nt database using the Galaxy web interface. I am using a Galaxy-generated FASTA file produced from a groomed FASTQ file using the 'FASTQ to tabular' and 'Tabular to FASTA' tools. When I try to use this as input for the Megablast tool, I get the "Required metadata values are missing" error. When I look at the attributes of the FASTA file, the datatype is indeed set to FASTA. I have tried downloading the FASTA file and reuploading it as a FASTA file explicitly with the same result. I also tried changing the FASTA width to 79, and trimming the records to 70nt each – not the problem. If I make a file containing only the first FASTA record, I get the same error. Any suggestions? Thanks! Elaine

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A Query
by Eva Carolina Rueda 20 Feb '14

20 Feb '14

Dear users, My name is Eva, and Im researcher in FHUC-UNL Argentina. My work is in population genetics of freshwater fishes. I use microsatellite loci to test genpop data. I was wondering if Galaxy contains STRUCTURE software (Bayesian method to define number of clusters in a sample). If the answer is yes, ¿How should I use it? Thank you so much for your help, Dra. Eva Rueda Proffesor FHUC-UNL CIC-CONICET --- Este mensaje no contiene virus ni malware porque la protección de avast! Antivirus está activa. http://www.avast.com

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Disable seeding using Galaxy
by Thierry Grange 20 Feb '14

20 Feb '14

Hello I would like to disable seeding when doing a sequence mapping using bwa. Apparently, this is commonly performed using the aln -l option set at a value higher than the read length, and is often set at values above 1000. In Galaxy, the default option is -1 for this parameter, and it is indicated that -1 corresponds to infinity. Does that mean that seeding can be disabled using -1, and that it is disabled by default on Galaxy? I don't obtain exactly the same thing using -1 or 16000 for this parameter, even though the difference is marginal. Thanks for your insights Thierry Institut Jacques MONOD Paris

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confusion from "Extract Genomic DNA (version 2.2.3) "
by Lu, Mengmeng 20 Feb '14

20 Feb '14

Hi Galaxy team, I recently met two problems when I used " Fetch sequences> Extract Genomic DNA" in Galaxy Main instance. I wanted to extract the exons according to the coordinates in a GFF3 file from my reference sequences (from history, and I specified the genome build) which are in FASTA format. But after checking the output, I found: 1. The first base of each extracted exon was missing in the output, so each extracted exon sequence is one nucleotide shorter than the real length. 2. Some extracted exons are correct,but some extracted exons are wrong. The questionable exons could not be found in the corresponding reference. I can not figure out where they are from. I tried to read the manual/warnings in the page. But I have no idea with my strange output. Could anyone give me some clues,please? Thanks. Best, Miranda

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CummeRbund - biological replicates problem
by Dottorini, Tania 17 Feb '14

17 Feb '14

Dear all, I would like to visualise by CummeRbund the Cuffdiff results obtained using the cufflinks/cuffdiff workflow on the Galaxy server. My samples include replicates data and when I ask for analysis to be done by CummeRbund, to compare replicates, I get error messages. From past postings I red that the Galaxy Cuffdiff does not allows you to download all the required files to be used by CummeRbund for replicate comparisons. As far as I know, the only way to overcome this problem is to run local computer Cuffdiff. I would like to know if anything has changed so far concerning Galaxy Cuffdiff output files and if there are other options instead of running local computer Cuffdiff to solve this problem. Any help would be appreciated Thank you Tania

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