Fuad Gwadry wrote:
Hi All
I am getting negative values when reading quality scores when I read data generated in bowtie. Has anyone run into the same issue when using data generated by bowtie ? My session info is below.
For the record, the development version of ShortRead has been changed to
return FastqQuality encoding of the quality scores, for both
readAligned, type="Bowtie" and for readFastq. The return type can be
selected using the argument qualityType="SFastqQuality", for instance,
for either command. This will be reflected in ShortRead version 1.3.24,
available from svn now and via biocLite (for those using the development
version of R) in a day or so.
Martin
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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