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

demultiplex Miseq data with separate index file.
by Philip Dean 27 Feb '12

27 Feb '12

I am using Galaxy main site to analyse MiSeq data of pooled samples. Essentially the run produces 3 fastq files consisting of R1, R2 read files and a separate index file. They are in the format below. R1: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0 Sequence data R2: @M00132:6:000000000-A0JG4:1:1:18014:1842 2:N:0:0 Sequence data Index: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0 CTCGGT + <@@DFD I would like to use Galaxy to demultiplex the samples and then analyse them individually. I have found barcode Splitter (version 1.0.0) on Galaxy however this tool requires the index to be found at the beginning of the sequence. Therefore I am attempting to add the index sequence onto the end of the sequence read data. FASTQ joiner (version 1.0.0) joins fastq files, however the fastqs to be joint must be distinguished by a /1 or /2 at end of sequence identifiers. Does anyone have any advice or experience of demultiplexing data in this format? Thanks, Phil DISCLAIMER: The information in this message is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, or distribution of the message, or any action or omission taken by you in reliance on it, is prohibited and may be unlawful. Please immediately contact the sender if you have received this message in error. Thank you.

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Convert SAM to bigwig
by Stephen Taylor 27 Feb '12

27 Feb '12

Hi, What is the 'official' method of converting a BAM file to a bigwig on the public server? I saw this post: http://gmod.827538.n3.nabble.com/SAM-to-bigbed-td3059499.html but it seems a bit long winded given the commonness of the operation. On our local galaxy we installed from the Tool Shed: BAM to BigWig Calculates coverage from a BAM alignment file Which seems the obvious choice to make available. Thanks, Steve

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Data not uploading in Local instance
by Luciano Cosme 27 Feb '12

27 Feb '12

*Hi Everyone, I have been running a Local Galaxy instance for a long time, but now I am having some problems with uploading data. I am getting the following error:* Can't create peek [Errno 2] No such file or directory: '/home/koala2/galaxy-dist/database/files/000/dataset_13.dat' * and from the Terminal:* 127.0.0.1 - - [25/Feb/2012:17:45:00 -0500] "POST /library_common/library_item_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/library_common/browse_library? sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp= galaxy&id=f2db41e1fa331b3e&page=1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" * I reinstalled Unbutu and still having the same issue. I also removed Postgresql 9.1 and reinstalled it. I that it might be an issue with postgresql and not Galaxy, but I am not an expert. Any suggestions will be appreciated. Thank you. Luciano *

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TopHat version in GALAXY
by Genaro Pimienta 27 Feb '12

27 Feb '12

Dear all: I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and CUFFDIFF crash upon starting. In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version integrated, while the TOPHAT website claims the latest version is 1.4.1. My question is which are the best/appropiate TOPHAT and CUFFDIFF versions? The error message I get is TOPHAT not recognized. Any other suggestions? Thanks, G.

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questions on directionality
by Maness, Nicholas J 27 Feb '12

27 Feb '12

Hi there, I apologize if this is covered in documentation or help threads. searched and it seemed it was not. I have several illumina rna-seq data sets that "should" be directional. It seems the directionality is very good, based on the visualization. First question is; in the visualization window, are the reads color coded by direction, i.e. are orange one direction and blue the other? If so, it looks like my data is >95% directional. Similar question, is there a way to quantify directionality of the data set? BTW, the data is RNA-seq data from rhesus macaques and i'm using the rhesus macaque genome build from UCSC. thanks very much, Nick Maness Tulane University

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Re: [galaxy-user] wrapper question prefix for output files.
by VICTOR M RUOTTI wisc-mail 24 Feb '12

24 Feb '12

Hi Peter,Thanks for the quick feedback. Sorry if I wasn't clear. Yes, I asking on how to set the labels for a file so instead of <data format="tabular" name="filename" label="genes-results"/> we can have a variable that comes from the interface set by the user so it can be like this? Say the user set the name from a text box to be "S" We can have S saved as $prefix, something like below. <data format="tabular" name="$prefix.filename" label="$prefix.genes-results"/> The files then will be labeled: S.genes-results They still be called dataset_547.dat but labeled based on the user's input? Victor On 02/23/12, Peter Cock wrote: > On Thu, Feb 23, 2012 at 5:46 PM, Victor Ruotti <ruotti(a)wisc.edu> wrote: > > Hi, > > I hope someone can help me on how to implement this into a wrapper. > > This kind of question is normally redirected to the galaxy-dev list. > > > We would like to add an option so the user can set a sample name > > which then be used for the prefix of the output files names. > > You have no control over the file names at all - Galaxy will assign > something like database/files/000/dataset_547.dat automatically. > The user never sees the file names anyway. > > Are you asking about how to control the description/caption shown > to the user in Galaxy? > > Peter

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Pre-processing of Illumina RNA-Seq paired end data
by Ravi Karra 23 Feb '12

23 Feb '12

Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically stuck while trying to pre-process my data prior to using Tophat/CuffDiff. For each sample, I have a read1 fastq file and a paired read2 fastq file. After using FASTQ Groomer, I trimmed the ends using FASTQ quality trimmer with a threshold quality score of 20 ans a window size of 1 (I think that will essentially lop off the end of the read until the quality score is >= 20). Next, I trimmed the adapters using Clip. What I am left with is a modified read1 fastq file and a modified read2 file, where the pairs are not in the same order and some reads are left without pairs. From what I have read, I don't think TopHat can incorporate paired end data that is out of order.. I tried to get around the ordering issue using FASTQ joiner, but this tool is not able to join the reads (return is 0 joined reads). I am not really sure why FASTQ joiner didn't work for me and am looking for suggestions of what to try next. Thanks! ravi

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merging databases
by De Gendt, Karel 23 Feb '12

23 Feb '12

Hi! Here's a really simple question, but I somehow can't find an easy answer in Galaxy. I want to merge two fastq files (they contain 2 sequencing runs of the same library, and I want to pool them). How do I do that in Galaxy? Thanks! Karel

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velvetoptimizer on galaxy toolshed
by Noa Sher 23 Feb '12

23 Feb '12

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Make a vcf file
by David Matthews 22 Feb '12

22 Feb '12

Hi, This may be a dense question, but how do we generate a vcf file from the public version of Galaxy? Am I missing something obvious? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk

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