[galaxy-user] ILLumina 1.9 Hiseq

2012-02-29 Thread Ateequr Rehman
Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is EncodingSanger / 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

Re: [galaxy-user] ILLumina 1.9 Hiseq

2012-02-29 Thread Jennifer Jackson
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

Re: [galaxy-user] ILLumina 1.9 Hiseq

2012-02-29 Thread Carlos Borroto
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

Re: [galaxy-user] ILLumina 1.9 Hiseq

2012-02-29 Thread Jennifer Jackson
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