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
>> **
>>
>>
>>
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>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
> ___________________________________________________________
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