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
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@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:
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Hi, I am using Mpileup from the Main Server (current version 0.0.1). In theory, this tool can generate two formats of output files: either a .bcf or a pileup. However, I couldn't find the option to select a .bcf file, even when I click on "Set advanced options". When run, the 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 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-31
On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard <fbesnard@biologie.ens.fr> 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 you only get the BCF output when "Genotype Likelihood Computation" is set to "Perform genotype likelihood computation". Hope it helps, Carlos
Hi Carlos, Thanks for your help: setting "Genotype Likelihood Computation" to "Perform genotype likelihood computation" do give a bcf in output rather that a pileup. Then I use "bcftools view" to convert this bcf to a standard vcf format. Fabrice Le 06/11/2013 20:32, Carlos Borroto a écrit :
On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard <fbesnard@biologie.ens.fr> 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 you only get the BCF output when "Genotype Likelihood Computation" is set to "Perform genotype likelihood computation".
Hope it helps, Carlos
-- 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: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-31
Hi, I am trying to connect to the Galaxy server via Filezilla in order to upload datasets. The connexion fails, with this message: "ECONNREFUSED - Connection refused by server". I have checked my password which works well to login to my account on the main server. Is it just temporal? 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: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-31
Hi Fabrice, Are you connecting to `usegalaxy.org`? This changed when we moved main.g2.bx.psu.edu to usegalaxy.org. Thanks, --nate On Nov 8, 2013, at 6:32 AM, Fabrice Besnard wrote:
Hi,
I am trying to connect to the Galaxy server via Filezilla in order to upload datasets. The connexion fails, with this message: "ECONNREFUSED - Connection refused by server". I have checked my password which works well to login to my account on the main server.
Is it just temporal? 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: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-31 ___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
participants (5)
-
Benjamin Osei-agyeman -
Carlos Borroto -
Fabrice Besnard -
Ido Tamir -
Nate Coraor