On 08/09/2011 14:17, Hans-Rudolf Hotz wrote:



On 09/08/2011 09:47 AM, Stephen Taylor wrote:
On 07/09/2011 20:22, Edward Kirton wrote:
seems unnecessary since illumina switched over to fastqsanger now.

http://www.illumina.com/truseq/quality_101/quality_scores.ilmn

Eventually...unfortunately we still get a lot of fastqillumina :-(


I might miss your point.....but why can't you use the fastq groomer tool?


- Duplication of data (disk space usage)
- Groomer is slow and puts more demands on CPU usage where it can be done 
easily on the fly by tophat
- Consistency (bowtie does it)

From the responses (or lack of :-)) we've been spurred on to change the wrapper. If there is interest we will commit it to the code base when done.

Cheers,

Steve
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