Hello,
We've processing several FASTQ files (Illumina, of course ;) ), and the FASTQ-Groomer is running for 2.5 hours now. The input files are ~4.5GB / 36nt .
First, Is any one else getting faster results ? maybe we're doing something wrong that can be improved.
Second, Is any one on the mailing-list have Illumina-capable versions of TopHat/Cufflinks, ones that don't require grooming ?
Thanks, -gordon
Second, Is any one on the mailing-list have Illumina-capable versions of TopHat/Cufflinks, ones that don't require grooming ?
This would be pretty easy to do:
(1) change the input datasets to be fastq rather than fastqsanger in tophat_wrapper.xml; (2) add an input to the wrapper to specify the input type, solexa 1.0, solexa/illumina 1.3+, sanger; (3) modify tophat_wrapper.py to accept and process the new input type.
FYI, I think Tophat assumes sanger format by default.
J.
galaxy-dev@lists.galaxyproject.org
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Assaf Gordon -
Jeremy Goecks