[protocols] Fwd: Kalamazoo Metagenome Assembly Question

[C. Titus Brown]

On Fri, Oct 25, 2013 at 08:36:49AM -0400, Adina Chuang Howe wrote:
> Hi folks,
> 
> 
> https://khmer-protocols.readthedocs.org/en/v0.8/metagenomics/1-quality.html
> 
> Is there a reason s2_se leftover from trimmomatic are excluded from this?
>  These files are generally smaller in my datasets (though I'm missing the
> biological reason for this).  As far as I know, these are the second pair's
> adapter-trimmed and possibly now unpaired.  I think they should be treated
> as s1_se?  i.e., quality trimmed and then concatenated with all single ends.

No good reason. I've just never had one generated.  This is on the list to
fix...

--t
-- 
C. Titus Brown, ctb at msu.edu