Re: [galaxy-user] How to know callable loci after variant calling in GATK ?

bly your > best option since this is the exact data that you want, and I am not > aware of any web-based implementations. > > But, this is still open for others to comment on! The web is a big place > & all input is welcome. > > Good luck with your project! > > Jen

[galaxy-user] How to know callable loci after variant calling in GATK ?

Hi all, Would someone know how to get the information on which areas of the genome are considered callable after a call with Unified genotyper from GATK (as a .bed or pileup file)? Thanks for your help/advice, Fabrice -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure

[galaxy-user] Implement GATK tool "Callable Loci" in Galaxy?

Hi all, First of all, thank you again for all your efforts to develop a project like Galaxy, that makes leading-edge bioinformatic tools available for non-bioinformaticians and wet-lab biologists like me ! I am using GATK Unified Geneotyper through the Galaxy main server to analyze variations fro

[galaxy-user] Pb with ftp connexion (FileZilla)

? Should I try to reset my password and give a new try? Thanks for assistance, best, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +3

Re: [galaxy-user] Samtools Mpileup output

20:32, Carlos Borroto a écrit : > On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard > wrote: > >> Would you have any advice to select the output format, or alternatively, >> a tool in Galaxy that can convert pileup into .vcf? >> > > Hi Fabrice, > > I believe yo

[galaxy-user] Samtools Mpileup output

program gives a pileup output format. Would you have any advice to select the output format, or alternatively, a tool in Galaxy that can convert pileup into .vcf? Many thanks for help, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex

Re: [galaxy-user] NGS jobs in hold?

> 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-user] Database of c_briggsae_WS230 for SnpEff

at I don't feel very comfortable with informatics (In other words, is the installation easy) ? many thanks in advance for your comments and advices, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office:

Re: [galaxy-user] Egg build failed for numpy 1.6.0

istinfo/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/ -- Fabrice Besnard Institute of Bio

Re: [galaxy-user] Problem with SAM-to-BAM conversion

friendly", which > was necessary for my application. > Hope this helps, > > Sam Politz > > -Original Message- > From: galaxy-user-boun...@lists.bx.psu.edu > [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Fabrice BESNARD > Sent: Monday, July 29, 2013 9

[galaxy-user] Problem with ftp connexion to Galaxy

ered that this was an issue happening with the new accounts created. Obviously, this issue has not been fixed yet, has it? If yes, could you indicate me to make my ftp connexion works now ? Thank you for your help !! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (I

[galaxy-user] Problem with SAM-to-BAM conversion

But when I click on the SAM-to-BAM tool, the header of the page says: SAM-to-BAM (version 1.1.2). I don't know if this matters or not. Could you please help me fixing this issue ? Many thanks ! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm