Quality Report

Question: Quality Report

5.1 years ago by

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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modified 5.1 years ago • written 5.1 years ago by Benjamin Osei-agyeman • 80

5.1 years ago by

Ido M. Tamir • 280

Austria

Ido M. Tamir • 280 wrote:

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

ADD COMMENT • link written 5.1 years ago by Ido M. Tamir • 280

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

ADD REPLY • link written 5.1 years ago by Fabrice BESNARD • 130

On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard 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

ADD REPLY • link written 5.1 years ago by Carlos Borroto • 390

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 ĂŠcrit : -- Fabrice Besnard Institute of Biology of the Ecole Normale SupĂŠrieure (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

ADD REPLY • link written 5.1 years ago by Fabrice BESNARD • 130

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

ADD REPLY • link written 5.1 years ago by Fabrice BESNARD • 130

Hi Fabrice, Are you connecting to `usegalaxy.org`? This changed when we moved main.g2.bx.psu.edu to usegalaxy.org. Thanks, --nate

ADD REPLY • link written 5.1 years ago by Nate Coraor ♦ 3.2k

5.1 years ago by

Benjamin Osei-agyeman • 80

Benjamin Osei-agyeman • 80 wrote:

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 Benjamin Osei-agyeman <benjy_osei@yahoo.co.uk>; To: Ido Tamir <tamir@imp.ac.at>; Cc: <galaxy-user@lists.bx.psu.edu>; Subject: Re: [galaxy-user] Quality report 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 Ido Tamir <tamir@imp.ac.at>; To: Benjamin Osei-agyeman <benjy_osei@yahoo.co.uk>; Cc: <galaxy-user@lists.bx.psu.edu>; Subject: Re: [galaxy-user] Quality report 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 Galaxy User list should be used for the discussion of mailing lists use the unified search at:

ADD COMMENT • link written 5.1 years ago by Benjamin Osei-agyeman • 80

On Wed, Nov 6, 2013 at 12:54 PM, Benjamin Osei-agyeman < Is the quality poor across the entire read, or just at one end? You can improve overall quality in two ways. By filtering out lower quality reads (the Filter by Quality tool or Filter FASTQ tool) or by trimming a portion of the reads (the FASTQ trimmer tool). It is important to understand that these tools work by throwing away data, you can't improve the overall quality of reads you already have. The FASTQC tool is telling you about the quality of your sequencing experiment. The only way to improve the overall quality is to do the experiment again. It means your quality score distribution is skewed. This is not necessarily a concern. -- James Taylor, Associate Professor, Biology/CS, Emory University

ADD REPLY • link written 5.1 years ago by James Taylor ♦ 470

Thanks a lot!!

ADD REPLY • link written 5.1 years ago by Benjamin Osei-agyeman • 80

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