[khmer] Counting kmers and disabling reverse complement

Lester Mackey lmackey at stanford.edu
Thu Jun 20 13:40:22 PDT 2013


Thanks Titus,

> 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?
>
> If I wanted to minimize the amount of memory used when k is small (i.e.,
when 4**k bytes is much smaller than 16GB), would setting hash_size =
4**(k-1) and n_tables = 4 or
hash_size = 4**k and n_tables = 1 be sufficient for a small false positive
rate?

Thanks,
Lester

>
> >  > >
> > > > > 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
> > > > >>
> > > > >> _______________________________________________
> > > > >> khmer mailing list
> > > > >> khmer at lists.idyll.org
> > > > >> http://lists.idyll.org/listinfo/khmer
> > > > >>
> > > > >>
> > > > >
> > >
> > > > _______________________________________________
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> > >
> > >
> > > --
> > > C. Titus Brown, ctb at msu.edu
> > >
>
> --
> C. Titus Brown, ctb at msu.edu
>
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