[khmer] Counting kmers and disabling reverse complement

[C. Titus Brown]

On Thu, Jun 20, 2013 at 08:01:41AM -0700, Lester Mackey wrote:
> Dear Jordan,
> 
> Does the counting hash have a built-in way to enumerate used hash table 
> entries without having to iterate over every hash table entry?

Err, no :).  Are you using ktable or counting hash?  If the latter then you
absolutely need to keep an explicit list of query k-mers.

> On a slightly related note, if I have 16GB of memory to work with, is it 
> advisable to choose hash_size = min(4**k, 16e9)/4 and n_tables = 4 when 
> calling new_counting_hash for k-mer counting?

http://khmer.readthedocs.org/en/latest/choosing-hash-sizes.html

best,
--titus

>  > >
> > > > On Fri, Jun 14, 2013 at 3:22 AM, Lester Mackey <lmackey at stanford.edu
> > >wrote:
> > > >
> > > >> Dear khmer Discussion List,
> > > >>
> > > >> If my goal is to obtain a vector of kmer counts quickly from a FASTA 
> > or
> > > >> FASTQ file, is there any reason to prefer ktable to one of your other 
> > data
> > > >> structures, like the counting hash table?
> > > >>
> > > >
> > > >> I've noticed that ktable hashes a kmer and its reverse complement to 
> > the
> > > >> same bin.  Is there an easy way to disable this feature (and thereby 
> > count
> > > >> each kmer and reverse complement separately)?
> > > >>
> > > >> Thanks,
> > > >> Lester
> > > >>
> > > >> _______________________________________________
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> > > >>
> > > >>
> > > >
> >
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> >
> >
> > --
> > C. Titus Brown, ctb at msu.edu
> >

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