Re: [galaxy-user] Quality report
Thanks a lot!! ___ 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/
Re: [galaxy-user] Samtools Mpileup output
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 you only get the BCF output when "Genotype Likelihood Computation" is set to "Perform genotype likelihood computation". Hope it helps, Carlos ___ 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/
Re: [galaxy-user] Quality report
On Wed, Nov 6, 2013 at 12:54 PM, Benjamin Osei-agyeman < benjy_o...@yahoo.co.uk> wrote: > 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? > 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. > And why is there a difference between the mean and median in the fastqc > report at each cycle? > It means your quality score distribution is skewed. This is not necessarily a concern. -- James Taylor, Associate Professor, Biology/CS, Emory University ___ 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/
Re: [galaxy-user] Quality report
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 ; To: Ido Tamir ; Cc: ; 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 ; To: Benjamin Osei-agyeman ; Cc: ; 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 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/ ___ 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/
[galaxy-user] Samtools Mpileup output
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: fbesn...@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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Quality report
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 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/ ___ 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/
[galaxy-user] Quality report
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/
