On 19/11/13 04:49 AM, Francois Le Fevre IG wrote:
> Dear ray community,
> I would like to know if ray is able to take as input both paired end
> files (option -p ) and single read ( -s), for the singleton reads that
> do not match with quality filter.
> Thanks
> Francois
>

Yes. And your paired files must have the same number of entries. In your case,
your single-end file should contain any read pair not matching your quality
filter.

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