[Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie

[Martin Morgan]

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