- galaxy-user - lists.galaxyproject.org

Google Summer of Code 2012 - Application Deadline on Friday 6th
by Robin Haw 02 Apr '12

02 Apr '12

The Genome Informatics group <http://gmod.org/wiki/GSoC>, is taking part in the Google Summer of Code (GSoC) <http://code.google.com/soc/> program. This year, the Genome Informatics group, will be organizing the joint efforts of Galaxy <http://galaxy.psu.edu/>, GBrowse <http://gbrowse.org/index.html>, Generic Model Organism Database (GMOD) <http://gmod.org/>, JBrowse<http://jbrowse.org/> , Reactome <http://www.reactome.org/>, Wormbase <http://www.wormbase.org/>, and PortEco <http://porteco.org/>. GSoC is a global program that funds student programmers around the world to write code for open source projects. More information about our project ideas and the GSoC program is available on the GMOD website <http://gmod.org/wiki/GSoC>. If you are a student interested in coding for our open source projects, then check out the links above and submit your project proposal as soon as possible. The application deadline is 6th April 2012. Robin Haw Genome Informatics Group Admin http://gmod.org/wiki/GSoC

1 0

April 2012 Galaxy Update
by Dave Clements 02 Apr '12

02 Apr '12

Hello all, The April 2012 Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04>is now available. *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#New_Papers> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Who.27s_Hiring>at six different institutions - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Upcoming_Events_and_Deadlin…> - GCC2012 Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#GCC2012_Update>, including - Abstract submission deadline is April 16. - Early registration is now open. - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Tool_Shed_Contributions>(at least 15 new repositories) If you have anything you would like to see in the May *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave C. -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

1 0

embl 66 genome for RNAseq analysis
by Karthik Srinivasan 02 Apr '12

02 Apr '12

Hi, How do I run Tophat and RNA-Seq analysis using the GRCH37- embl 66 genome? I noticed there is no input for this genome version. Can I construct a reference genome from the following embl format source sequences: ftp://ftp.ensembl.org/pub/release-66/embl/homo_sapiens/, and map it against my RNAseq data? Regards, Karthik Karthik Srinivasan | Senior Application Engineer P:HYPERLINK "tel:+912242554282"+912242554282 | M:HYPERLINK "tel:+919987014704"+919987014704 Oracle Health Sciences Global Business Unit 6'th Floor, Silver Metropolis, W.E.Highway, Goregaon(E) | 400063 Mumbai

2 1

CummeRband in Galaxy platform
by Bomba Dam 30 Mar '12

30 Mar '12

Hi Galaxy team, Are there any plans to add the CummeRband tool in the Galaxy platform. It would be very nice to have it within Galaxy, this will help people like us (Biologists, without much programming knowledge) to do the complete RNA-seq analysis and visualize the data in graphical forms Cheers. Bomba --

3 2

correct input into the minimum alignment count
by vang0280＠umn.edu 29 Mar '12

29 Mar '12

Dear all, I changed the minimum alignment count to: 100, 400, and 1000 minimum alignment differential expressed genes 100 4, 000 400 2,000 1000 (default) 1,000 I was wondering, which minimum alignment we should go with? It would appear the higher the alignment, the amount of differential expressed genes are decreased. I was also wondering if the minimum alignment refers to the # of reads per sequence? Is this true? Also how are the FPKM and the minimum alignment are related? Thanks, Bao

2 1

how to view the Tophat output ?
by Xu, Jianpeng 29 Mar '12

29 Mar '12

Hi , I have installed our local galaxy and tried to run some programs. I have run the Tophat with RNA-seq data. There are two output files: accepted_hits, and splice_junctions. Can you tell me how to view the results files? Is there a tool on galaxy that can be used to view the result ? Can I use IGV to view it ? Thanks a lot. Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

3 2

how to view the tophat output ?
by Xu, Jianpeng 29 Mar '12

29 Mar '12

Hi , I have installed our local galaxy and tried to run some programs. I have run the Tophat with RNA-seq data. There are two output files: accepted_hits, and splice_junctions. Can you tell me how to view the results files? Is there a tool on galaxy that can be used to view the result ? Can I use IGV to view it ? Thanks a lot. Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

1 0

https://biocloudcentral.herokuapp.com/launch site is down
by mailing list 28 Mar '12

28 Mar '12

Hi guys, I was unable to load this site today: https://biocloudcentral.herokuapp.com/launch Please tell me it's still available. I spent long time writing our documentation to tell users how to use it :-( thanks, Greg

3 3

Cow Genome update in Tophat
by Aranday-Cortes, Elihu 27 Mar '12

27 Mar '12

Hi Galaxy Team, I'd like to use Tophat but the last version of the cow genome is not listed (BotsTau7). Tha last version is listed is BosTau4 . any chance for an update? Thanks Elihu

3 3

RV: Subdivide peaks
by Mónica Pérez Alegre 27 Mar '12

27 Mar '12

Hi I´m working with data from tiling array (S.cerevisiae). I need to analyze the distribution of the enrichment signal along the length of all ORFs. So I want subdivide the genomics intervals into 10 segments independent of ORF size. Are there any tools in galaxy for this? Thanks for the helpful Regards ☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications Mónica Pérez Alegre, PhD Genomics Unit CABIMER-CSIC Edif. CABIMER - Avda. Américo Vespucio s/n Parque Científico y Tecnológico Cartuja 93 41092 Seville-SPAIN Tlf: +34 954 467 828 Fax: +34 954 461 664 www.cabimer.es<http://www.cabimer.es/> http://www.cabimer.es/web/es/unidades-apoyo/genomica

1 0