[khmer] Partitioning: are resulting lumps that different from each other?

[YiJin Liew]

Hi Adina,

Thanks for the reply, and for clarifying the structure of the dist file!
I apologise for using the terms "partition" and "group" loosely in the past.

Unless I have misinterpreted your reply, it seems that my blast analysis
has been misunderstood. I DID NOT blast the Iowa corn groups against
each other. I blasted them, individually, against *nt*, with the hopes
of (crudely and quickly) checking the composition of reads in each group
(i.e. 10% came from organism A, 5% came from organsim B, 3% from C,
...). I concur with you that blasting them against each other makes
little sense.

If partitioning worked well, a reasonable hypothesis would be that
different groups would have markedly different compositions of reads -
reads from organism A might be a majority in group0000 for instance,
while reads from B predominate in group0001. What I see from my tests,
however, seem to refute this: groups0000, 0001 and 0002 have very
similar read compositions. You get lots of Rhodobacter stuff, followed
by Streptomyces, then Bradyrhizobium, etc.

My issue with this is that khmer suggests that the individual group
files should be assembled individually. What I suspect is that you'd
probably get very similar assembly outputs for the groups that hit
--max-size (I haven't tried that out, though). I have no doubt that the
biggest group would be different from the others, though. My dataset
produced a small group and a big group post-partitioning, and I obtained
very different sequence proportions when I carried out a similar
analysis on them.

Let me know if you'd like more details on how my blast test worked. Thanks!

Yours
Yi Jin

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