April 2013 - galaxy-user - lists.galaxyproject.org

raw count of genes
by Els Willems 11 Apr '13

11 Apr '13

Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-informatics field. I performed an RNA-Seq experiment with single end 50 bp reads to find differential gene expressions between different groups. I have mapped this data with Tophat. Does anyone know how I can get the raw data count out of galaxy in a tab-delimited file? I would like to perform a statistical analysis in other software, without the RPKM normalization that cufflinks offers. Thank you very much. Have a nice day. Yours Sincerely, Els --- Ir. Els Willems KU Leuven Department of Biosystems Division Livestock - Nutrition - Quality Laboratory of Livestock Physiology Kasteelpark Arenberg 30 bus 2456 B - 3001 Heverlee T (+32) 016 32 17 29 F (+32) 016 32 19 94

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Are reads of 36nt in length long enough to accutatly map on splicing junctions?
by Du, Jianguang 10 Apr '13

10 Apr '13

Hi All, I have a very basic question. I have RNA-seq datasets of several cell types and want to compare the alternative splicing events between cell types. The reads are 36nt in length. Are these reads long enough to map on the splicing jucntions accurately when I run Tophat with stringent parameters (no mismatch)? Thanks. Best, Jianguang Du

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merging fastq files
by Thompson, Andrew 10 Apr '13

10 Apr '13

Hi I have received Illumina paired-end genome sequence data as a .tar file. When unpacked the data for each genome accession is split into about 100 fastq files. Total of about 37 Gpb per genome. Can you recommend the best way to organise this data prior to mapping to reference genome? I can concatenate unpacked files using DOS command line into forward and reverse before uploading: is this the best approach? Is there a tools that will start with the .tar file? Andrew

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Parameters for merging BAM files
by Du, Jianguang 10 Apr '13

10 Apr '13

Hi All, I want to merge the Tophat output (Accepted Hits) of Several datasets. I want the merged BAM file has the exact format as the individual input BAM files, should I check "Merge all component bam file headers into the merged bam file"? Thanks. Have a nice weekend. Jianguang

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Using segments of sequences as a reference genome - Bowtie for Illumina
by Veranja Liyanapathirana 10 Apr '13

10 Apr '13

Dear all, My problem seems like something that should have a very simple solution from my end and due to my lack of knowledge in bioinformatics, I am probably messing up with the workflows. The experiment I run is one where we used Miseq to sequence amplicons of a multiplex PCR. We introduced an inhouse barcodeto our PCR products via an adaptor. Miseq data was demultiplexed for the Illumina barcodes using Miseq reporter on intrument software by our service provider and I am trying to run the rest of the process on Galaxy web port with no command prompt programming. The data for R1 and R2 was imported, and then I used barcode splitter to de-multiplex the amplicons after quality triming. (I did not use FASTQ groomer as Miseq data is supposed to be Sanger FastQ than Illumina). Then the sequence trimmer was used to trim the barcode+adaptor sequences. The results of this were re-uploaded and designated as FASTQ for alignment. Now for the reference genome, as our aplicons are of from different sequences, we have segmented FASTA sequences in one file with different FASTA identifiers. When this file was input as the reference genome and mapping was performed using Bowtie for Illumina, the mapping went on with no errors. I could filter the alignment file using SAM filters too. But I can not do any more downstream visualozations, not even SAM to BAM conversion. I suspect that this may be due to an error in the way that the reference genome was formulated but can not get around to figure it out. I would be extremely grateful if you could help me with this issue. I tihnk if I string together the sequences as one it would work, but converting this back for interpretation becomes an issue then. Thank you, Kind Regards, Veranja Veranja Liyanapathirana Graduate Student (Microbiology)

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problem using Depth of Coverage (GATK)
by Gema Sanz 09 Apr '13

09 Apr '13

Hello, I´m trying to use depth of coverage to check the coverage of my reads. I already have the bam files (created with sam to bam) but they are still not recognized by depth of coverage and I got this error message: "Sequences are not currently available for the specified build" I used "human (homo sapiens) hg19 full" for mapping but I can´t select it, it only allows b37 version. I tried to change the build in edit parameters to b37 and then it is recognized but I got another error at the end of the analysis. Any suggestions? Thank you very much in advance Gema

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files upload helo
by Dipanjana Datta De 09 Apr '13

09 Apr '13

hello, last time i uploaded these files they were up quckly, but now it seems to run forever, please help. is there something wrong with the server?? -- *Dipanjana Datta De* *Postdoctoral Fellow* *Department of Pharmacology and Toxicology* *Virginia Commonwealth University* *Richmond, Virginia*

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tophat job help
by Dipanjana Datta De 09 Apr '13

09 Apr '13

Hi, I have been running a tophat job and it seems to run forever, its now 24 HRS . I do not understand, is it that i have done something wrong, the other tophat job took only 6 hrs. please help regards, Dipanjana -- *Dipanjana Datta De* *Postdoctoral Fellow* *Department of Pharmacology and Toxicology* *Virginia Commonwealth University* *Richmond, Virginia*

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Extracting sequences for transcripts from reference genome
by Lizex Husselmann 09 Apr '13

09 Apr '13

Dear Galaxy community I'm new to galaxy and would like to ask the following: I have trimmed, QC'ed my data received from Illumina HiScan SQ, paired and single end data. Mapped using Tophat, run cufflinks, cuffmerge and cuffdiff. I would like to analyze the gene_exp.diff file by extracting the significant transcripts. I've used grep "yes" to extract only the significant transcripts. From this info I have the locus start and end coordinates of each transcript for example "XLOC_000544 XLOC_000544 - chr1:12763969-12765675 C0 C4 OK 3.16487 1628.25 9.00696 -4.57022 4.8722e-06 0.00905256 yes". How can I go about to extract this information/or sequence from the reference genome. Kind regards Lizex This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 000 604 Fax number : 0800 00 7788 Email address : arc(a)tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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GCC2013 Talk Abstract Submission closes this Friday
by Dave Clements 09 Apr '13

09 Apr '13

Hello all, This is a final reminder that the *deadline for submitting an oral presentation abstract is this 12 April, this Friday*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. And in case you missed the announcement about GIgaScience and GCC2013 talks: We are pleased to announce that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience <http://www.gigasciencejournal.com/>* and that BGI<http://www.genomics.cn/en/index>will generously cover the article processing fees for these articles. See the announcement <http://wiki.galaxyproject.org/News/GigaScienceGalaxyCFP>for details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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