[khmer] filter-below-abundance typical discard rate

[Chuck]

I'm curious about typical values that people are seeing with
filter-below-abundance. With the default cutoff (50) I was discarding ~50%
of bp (after normalizing with C=20). If I increase the cutoff to 225 the
discard rate drops to 25%. I thought I was rigorously adapter trimming my
reads (I generally use scythe with default parameters and I monitor the
output fairly closely). Is this way outside the developers' experience?

Also, at a cutoff of 235, I discard 0%. Not sure how to interpret this. I
realize that you don't count kmers above 255 by default with
load-into-counting. It seems that I don't have any kmers at the ends of
reads at a depth >=235 but I trim much more data with what seems like a
small change in the cutoff value from 235 to 225. Also, 235 < 255 :) .

Thanks,

-Chuck
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