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 <jen@bx.psu.edu> *To:* Ateequr Rehman <ateeqrr@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
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 **
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