galaxy-user November 2013

galaxy-user@lists.galaxyproject.org

46 participants
45 discussions

multiple output tool in workflow
by Jun Fan 09 Nov '13

09 Nov '13

Hi all, I am trying to creating a workflow from history. One of the tool used generates multiple outputs in the format of gff3, fasta and sam. Gff3 will be visualized in IGV and the fasta file is doing further BLAST analysis. Now the problem is that the automatically generated workflow does not connect the having-multiple-output tool and the BLAST tool. I failed even I tried to connect these two tools in the workflow by hand. I am guessing this is due to only the main output type (gff3) is recognized in the workflow. How could I solve this problem? Best regards and have a nice weekend! Jun

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Quality report
by Benjamin Osei-agyeman 08 Nov '13

08 Nov '13

Hi, After obtaining a quality report in galaxy I found out that there is a difference between the mean and median at each cycle. How can this difference be reduced using galaxy? Thanks in advance Benjy

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How do I import protein coding genes location from UCSC?
by Himanshu Sharma 08 Nov '13

08 Nov '13

I have to import into Galaxy annotations of coding genes from the UCSC genome browser and then use the "Operate on genomic intervals" set of tools to remove transcripts that overlap with coding genes from my gtf file . How should I go about doing it?. Thanks, Himanshu

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Galaxy Pages - importing/downloading embedded data.
by Mohammad Heydarian 08 Nov '13

08 Nov '13

Hi All, Hope things are groovy. I am in the process of setting up a Galaxy page on the main server to host our NGS data. I am embedding the various datasets and they are showing up and viewable, but there is no way to import (or download) the data. Am I correct, or is the import button hidden on my screen? Would publishing the Page enable import of the data? Many thanks in advance, we are looking forward to utilizing Galaxy Pages and making our data accessible. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205

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conditional statement in compute tool
by Leontovich, Alexey A., Ph.D. 08 Nov '13

08 Nov '13

Hello! I have the same question as Ido Tamir had about a year ago: Dec 07, 2012; 9:53am [Ido Tamir] <http://user.list.galaxyproject.org/template/NamlServlet.jtp?macro=user_node…> Ido Tamir<http://user.list.galaxyproject.org/template/NamlServlet.jtp?macro=user_node…> conditional in Compute tool Hi, is it possible to do a conditional in the compute tool? something like: "a" if c1 == 4 else "b" or if c1 == 4 "a" else "b" or c1 == 4 ? "a" else "b" thank you very much, ido Thank you very much, Alex

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Bowtie raw input
by Jonathan Glass 08 Nov '13

08 Nov '13

Hi There Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using both Bowtie 1 and Bowtie 2. Im currently using publicly available data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28755) which is not available in FASTQ format - only the raw sequences with the read count. Is there a way to set the input data for bowtie to raw, as is possible using the terminal? Or is there a way to convert a raw sequence to FASTQ (not sure if this would work, but it might be possible if I assigned accession numbers to each sequence and made all the quality scores identical)? Thanks very much Jonathan Glass Disclaimer - University of Cape Town This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.

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problems with TOPHAT in Galaxy
by Amit Pande 08 Nov '13

08 Nov '13

Hi, I am trying to align long RNA fatsq formatted files from ENCODE project generated by CSHL. The problem I am encountering is that there is no XS file being generated which can be taken for further processing with samtools. Kindly help. warm regards, Amit.

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Contents of a SAM file
by Benjamin Osei-agyeman 07 Nov '13

07 Nov '13

Hi What are the contents of a SAM file after Bowtie has been run? Does it contain all reads or only those reads mapped to the genome? Thanks Benjy

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Coding and non coding exons
by Benjamin Osei-agyeman 07 Nov '13

07 Nov '13

Hi, I am very new to the UCSC browser, I want to find the number of coding and non coding exons for the gene S100A2 using hg19 gene symbol? Also how do I find the disease associated with this gene? Thanks in advance Benjy

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Re: [galaxy-user] Quality report
by Benjamin Osei-agyeman 07 Nov '13

07 Nov '13

Hi, The report was obtained after running fastqc on my data. However after looking at the report statistics, the Quality is not good in the Per Base Sequence Quality and there is a difference between the mean and median at each cycle. How can the quality be improved? And why is there a difference between the mean and median in the fastqc report at each cycle? Benjy From: Benjamin Osei-agyeman <benjy_osei(a)yahoo.co.uk>; To: Ido Tamir <tamir(a)imp.ac.at>; Cc: <galaxy-user(a)lists.bx.psu.edu>; Subject: Re: [galaxy-user] Quality report Sent: Wed, Nov 6, 2013 5:31:22 PM The report was obtained after running fastqc on my data, I found out that the quality of the report is not good and that the mean and median are different at each cycle. Please how can the difference between the mean and median be improved as well as improving the overall quality From: Ido Tamir <tamir(a)imp.ac.at>; To: Benjamin Osei-agyeman <benjy_osei(a)yahoo.co.uk>; Cc: <galaxy-user(a)lists.bx.psu.edu>; Subject: Re: [galaxy-user] Quality report Sent: Wed, Nov 6, 2013 4:38:15 PM Please be more specific about which quality of what gets reported. Why do you think its important to reduce the difference between mean and median? best, ido On Nov 6, 2013, at 4:50 PM, Benjamin Osei-agyeman <benjy_osei(a)yahoo.co.uk> wrote: > Hi, > After obtaining a quality report in galaxy I found out that there is a difference between the mean and median at each cycle. How can this difference be reduced using galaxy? > > Thanks in advance > Benjy > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/

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galaxy-user November 2013