galaxy-user July 2011

galaxy-user@lists.galaxyproject.org

67 participants
78 discussions

RNA-seq Galaxy workflow for PE barcoded samples?
by Whyte, Jeffrey 13 Jul '11

13 Jul '11

Hello, I posted to the seqanswers forum, but have not received any feedback. I am working with RNA-seq Illumina data files in Galaxy (http://main.g2.bx.psu.edu/). The two files are 100bp paired-end reads, multiplexed with barcoding to distinguish samples. The barcodes are the first four bases of the sequences in the s_7_1_sequence.txt file. Would the following Galaxy workflow be correct? 1. Upload both s_7_1_sequence.txt and s_7_2_sequence.txt to Galaxy with the reference genome selected 2. Run NGS: QC and manipulation --> FASTQ Groomer on each file to convert to Sanger FASTQ 3. Run NGS: QC and manipulation --> FASTQ joiner to combine the data from the two files 4. Run FASTX-TOOLKIT FOR FASTQ DATA --> Barcode Splitter to generate separate FASTQ files for each barcode group 5. Run NGS: RNA Analysis --> Tophat to map the reads from each group to the reference genome The problem I am having is that if I select paired-end for the library in Tophat, it requests two FASTQ files. Would I have to use FASTQ Splitter to separate the joined FASTQ files? If there is a more standard way to handle these types of barcoded files, I would appreciate hearing about this workflow. Thanks very much in advance, jjw P.S. Galaxy is an incredibly useful resource. Thanks!

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problem in saving visualizations in trackster
by suman pal 13 Jul '11

13 Jul '11

Hello, I am registered as jigassa(a)yahoo.com in Galaxy main. recently I am trying to save visualizations in Trackster and repeatedly getting a message unable to save visualization.Is this something related to my PC memory ?This is in reference to RNAseq track visualization while adding tracksGalaxy tutorial):a) accepted hits track bam fileb) splice junction bed filec) and the table browser chr19 ref seq track Kindly see where the problem is? sincerelySuman

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Workflow assistance
by Kevin Pawlik PhD 13 Jul '11

13 Jul '11

After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following: I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome. Many thanks, Kevin

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Galaxy Events Page and Google Calendar
by Dave Clements 13 Jul '11

13 Jul '11

Hello all, The new Galaxy wiki includes a Galaxy Events<http://wiki.g2.bx.psu.edu/Events>page ( http://wiki.g2.bx.psu.edu/Events) that lists upcoming events (such as ISMB/ECCB 2011 <http://wiki.g2.bx.psu.edu/Events/ISMB-ECCB-BOSC%202011> and the Workshop on Comparative Genomics<http://www.molecularevolution.org/workshops/WCG#wcgna>) that have Galaxy related content. The page also contains a link to the new Galaxy Events Google Calendar<https://www.google.com/calendar/embed?src=mq93blfvdoosh5unpmivu4kh1c%40grou…>, that lists events and deadlines that may be of interest to the Galaxy community. For example, this week there are 5+ events going on and these 5 deadlines as well: <http://psb.stanford.edu/> - PSB 2012 <http://psb.stanford.edu/> abstracts (were due Monday) - Beyond the Genome <http://www.beyond-the-genome.com/program.html>abstract and early registration (Friday) - GIW 2011 <http://www.kobic.re.kr/giw2011/> abstracts (Friday) <http://meetings.cshl.edu/courses/c-ecg11.shtml> - Computational & Comparative Genomics Course<http://meetings.cshl.edu/courses/c-ecg11.shtml>application (Friday) <http://meetings.cshl.edu/courses/c-seqtech11.shtml> - Advanced Sequencing Technologies & Applications Course<http://meetings.cshl.edu/courses/c-seqtech11.shtml>application (Friday) If you know of events that either have significant Galaxy content, or are of interest to the overall community, please send them to outreach(a)galaxyproject.org and they will be added to the Events<http://wiki.g2.bx.psu.edu/Events>page and the calendar. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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finding open reading frames and corresponding genes
by Joanne Rampersad 13 Jul '11

13 Jul '11

Hi I am sequencing a bacterial genome and have assembled my Illumina reads (40 bp single) using bowtie with a reference genome. This generated a sam file. I would like to obtain a listing of the open reading frames from the bacterial genome and the corresponding genes that they are most similar to. Can you please give the tools/steps necessary to do this? many thanks Jo

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Galaxy @ ISMB/ECCB, 3DSIG, and BOSC
by Dave Clements 12 Jul '11

12 Jul '11

Hello all, Galaxy will have a large presence at ISMB/ECCB, 3DSIG, and BOSC, all of which start this week in Vienna. Galaxy related content includes (at least): 1 Galaxy organized workshop on "Genomics for Non-Model Organisms" featuring 4 talks, 7 additional talks at ISMB/ECCB and BOSC, and 3 Posters at ISMB/ECCB and 3DSIG That's enough to fill a wiki page and a flier (and so it has :-). See http://wiki.g2.bx.psu.edu/Events/ISMB-ECCB-BOSC%202011 for a listing of all known Galaxy-related content and a flyer you can print out and take with you. Watch Twitter (@galaxyproject, #usegalaxy) during the conference for updates and reminders. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Workflow API
by Simon Lank 12 Jul '11

12 Jul '11

Hi Again Galaxy team. I'm attempting to use the new workflow API, which I understand is still in development. I created a test workflow with a single input, and was able to use 'example_watch_folder.py' to successfully execute it as a history and get the output to a specified location. My question is how I can modify the script to accept multiple inputs (i.e. how do I define which files in the input folder I want to be each input) and if there's a way to specify runtime parameters. For instance, the workflow I want to execute has a filter step on a tabular input item as one of the later steps which needs to be defined at runtime. How would I specify this in the 'watch_folder.py' parameters? or is this not possible yet? FYI, I know perl but not python, so ultimately I want to wrap the python scripts into a larger perl script to execute recursive workflows. Thanks for all your help. Galaxy is an amazing tool and the workflow API is a fantastic improvement. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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exporting HTML with associated files
by Joern Toedling 12 Jul '11

12 Jul '11

Hello, I have a question regarding exporting data from Galaxy. I have written a tool which creates an HTML page and an associated directory containing pictures and text files. However, if I want to export or share the result files, only the resulting HTML is shared/exported and not the associated folder, meaning other people can see the HTML but without the images or included/linked text files. Is there are a way around this? Do I need to export the data in another format or change the output format of the tool? Any suggestions would be appreciated. Thanks, Joern -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511

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Re: [galaxy-user] Hi
by Ido Tamir 12 Jul '11

12 Jul '11

On Jul 11, 2011, at 10:04 AM, YOGESH OSTWAL wrote: > thanks a lot. > > Sorry for disturbing you again. > > Before starting with the actual data, can I try this analysis with already available IP and input files of datasets of illumina from NGS repository? why shouldn't you? select something from geo or from a paper. http://www.ncbi.nlm.nih.gov/geo/ Use a download manager to download the big files. best, ido

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Exome anylisis by Galaxy
by Eduardo Calpena 12 Jul '11

12 Jul '11

Hello everyone, I am a new user of Galaxy. I have received the data from an exome of 4 samples. I have two reads from each sample. I have seen the Live Quickies, and I have a general idea that I want to do. I want to find every change in the exome of these samples. Then apply a filter to discard all the known SNPs. Finally I want to keep only the changes that are in common in the four samples and apply a scoring of possible pathogenic mutations (PhiloP, SIFT,…). Is it possible? Anybody can help me by sending me a step by step protocol of how can I do this analysis? And another question, could I do all these previous steps with each individual, independently, or should I do it with the four samples at the same time? Thanks to all of you. I look forward to hearing from you. Edu _ _ Eduardo Calpena Corpas, PhD Student Instituto de Biomedicina de Valencia (IBV-CSIC) C/Jaime Roig Nº 11 Valencia. E-46010 (SPAIN). TEL: +34 96 339 1760. FAX:(+34) 96 369 0800

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galaxy-user July 2011