Re: [galaxy-user] ILLumina 1.9 Hiseq
Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, Thanks ** ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hi Jen, I have a related question. If Illumina 1.9 is already in Sanger format, is it still necessary to groom the FASTQ files for TopHat? Would it be enough to directly change the data type to Sanger without grooming? Thanks, Carlos On Wed, Feb 29, 2012 at 10:57 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, Thanks ** ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/ ___ 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hi Rich, Tools will allow grooming to be skipped if the data is already in fastqsanger or fastqcssanger format (as appropriate). This can be set at upload or on the Edit Attributes form (pencil icon). For Illumina, these would be data resulting from the CASAVA 1.8+ pipeline. For Illumina 1.5, select Illumina 1.3-1.7 on the FASTQ Groomer tool form to properly format the data. Thanks for bringing up a good topic! Not having to groom can save both time and disk space. Best, Jen Galaxy team On 2/29/12 8:24 AM, Richard Mark White wrote: I have a question about the groomer. Do all Illumina runs need to be groomed, or are there situations where it can be skipped?? (My data says illumina 1.5, so ive been picking input type as illumina 1.3-1.5.) rich *From:* Jennifer Jackson j...@bx.psu.edu *To:* Ateequr Rehman atee...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Wednesday, February 29, 2012 10:57 AM *Subject:* Re: [galaxy-user] ILLumina 1.9 Hiseq Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, Thanks ** ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
