On Tue, May 3, 2011 at 10:00 AM, Robin Mjelle robinmjelle@gmail.com wrote:
Dear User,
I am trying to use the tool "Compute quality statistics" in galaxy on Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed Quality format converter on the data set and the format is now qualillumina. Despite of this, galaxy don't recognize any dataset in the workflow to use as input into quality statistics. Any idea why my dataset is not accepted as input?
Best,
Robin
Looking at the XML wrapper, it expects fastqsanger ONLY. See fastx_toolkit/fastx_quality_statistics.xml
It could in theory take fastqillumina or fastqsolexa as well, I thought there was an open bug report on this issue but I can't find it right now. Certainly fastx_clipper.xml was updated to use the -Q 33 switch only for Sanger quality scores, and from a quick check all the other FASTX tools have this fix except fastx_quality_statistics.xml
Peter