- galaxy-user - lists.galaxyproject.org

problems with TOPHAT in Galaxy
by Amit Pande 07 Nov '13

07 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 06 Nov '13

06 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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Re: [galaxy-user] galaxy-user Digest, Vol 89, Issue 4
by Cory Dunn 05 Nov '13

05 Nov '13

Dear Graham, Thanks for the info. However, my problem is that the "Tool Version" field is completely empty in my history items (eg. Tophat2, Cuffdiff). I suppose I can check the dependancies list you described, but it would be important to know precisely which version was run on any given query. Best regards, Cory Message: 3 > Date: Tue, 5 Nov 2013 09:45:19 +0000 > From: "graham etherington (TSL)" > <graham.etherington(a)sainsbury-laboratory.ac.uk> > To: Cory Dunn <cdunn(a)ku.edu.tr>, "galaxy-user(a)bx.psu.edu" > <galaxy-user(a)bx.psu.edu> > Subject: Re: [galaxy-user] Cuffdiff version not apparent > Message-ID: > <CE9E6D0A.21768%graham.etherington(a)sainsbury-laboratory.ac.uk> > Content-Type: text/plain; charset="Windows-1252" > > Hi Cory, > A list of Galaxy dependancies can be found on the wiki at: > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > ...although many tools allow a range of tool versions. > > You can also identify the information about the specific tool versions by > clicking on the View Details ?i? icon of a history item created by that > tool and looking at the Tool Version field. > If you?re using the Galaxy public server (https://usegalaxy.org/) then > clicking on the ?i? icon of a cuffdiff output file will show: > > Tool Version:cuffdiff v2.1.1 (4046M) > Hope this helps. > > Cheers, > Graham >

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Cuffdiff version not apparent
by Cory Dunn 05 Nov '13

05 Nov '13

Dear Galaxy Staff: I was wondering which version of Cuffdiff is currently running on Galaxy. The wrapper version is 0.0.6, but I did not see the actual version of the underlying software under the "Tool Version" field (please see attached screen grab). Thanks for your help, Cory Dunn [image: Inline image 1]

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Nov 04, 2013 Galaxy Distribution
by Jennifer Jackson 04 Nov '13

04 Nov '13

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Re: [galaxy-user] Galaxy's Tophat 2 -GTF option
by Jennifer Jackson 01 Nov '13

01 Nov '13

Hi Zain, Annotations are used with Tophat2 the same way that they are with Tophat. Open up the full parameters on the tool form and change the option "Use Own Junctions:" to "Yes". Here you can now supply gene models as set related parameters. If actually performing this operation is problematic and producing errors, please submit a bug report, leaving inputs and outputs undeleted, so that we can troubleshoot. The wrapper is still somewhat new. Hopefully this helps & have a nice weekend, Jen Galaxy Team Jennifer Hillman-Jackson http://galaxyproject.org > On Nov 1, 2013, at 3:22 PM, Zain A Alvi <zain.alvi(a)student.shu.edu> wrote: > > Hi Jenn, > > I hope this reaches you well. I was trying to use tophat 2 on the public Pennsylvania Galaxy server and noticed that I was not able to supply the GTF file. Although it lists that providing GTF file is an option on the bottom of the tophat 2. I was wondering if it possible to add the option to provide an GTF file for Galaxy's Tophat 2. I have attached a screen shot for your kind review as well. > > I would really appreciate it if it was possible. > > -G/--GTF [GTF 2.2 file] > Supply TopHat with a list of gene model annotations. > TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will > attempt to align reads to these junctions even if they would not normally be covered by the initial mapping. > > Sincerely. > > > Zain > <Galaxy_Tophat2_GTF.jpg>

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Grouping Histories into related Projects
by Avery DeVries 01 Nov '13

01 Nov '13

Hello, I was wondering if there way any way to group related histories into "Projects" (like a home directory and sub-directories). Currently, I have several annotations/analyses in separate histories related to the same dataset (i.e. one for gene annotation, one for ENCODE elements, etc) and as you can imagine, as I have several other datasets each with separate histories for each analysis I conduct, my Saved Histories page can get pretty convoluted. I would like to keep them in separate histories so I can easily find separate analyses, but I really wish there was a way to group them together so I could parse through my long list of histories quickly. Is this possible to do? Thank you so much Avery *Avery DeVries* africker(a)email.arizona.edu

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November 2013 Galaxy Update Newsletter
by Dave Clements 31 Oct '13

31 Oct '13

Hello all, The November 2013 Galaxy Update is out<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11> : *Highlights:* - Two new public Galaxy servers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#New_Public_Servers> : CoSSci: Complex Social Science Gateway<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#CoSSci:_Complex_Social_…> (which has *nothing* to do with biology), and BioCiphers Lab Galaxy<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#BioCiphers_Lab_Galaxy> . - 53 new papers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#New_Papers>, including "Expanding roles in a library-based bioinformatics service program: a case study," "DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data," and "Ten Simple Rules for Reproducible Computational Research" - Who's hiring<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Who.27s_Hiring> - Upcoming Events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Other_Events>, including - Save these dates! GCC2014: June 30 - July 2, Baltimore<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#GCC2014:_June_30_-_July…> - Galaxy Day, December 4, Paris<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Galaxy_Day.2C_December_…> - UC Davis Bioinformatics Boot Camps<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#UC_Davis_Bioinformatics…> - Lifeportal launched at the University of Oslo<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Lifeportal_at_the_Unive…> - Tool Shed contributions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Tool_Shed_Contributions> If you have anything you would like to see in the next *Galaxy Update<http://wiki.galaxyproject.org/GalaxyUpdates> *, please let us know. Dave Clements and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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