[khmer] Counting kmers and disabling reverse complement

Lester Mackey lmackey at stanford.edu
Thu Jun 20 08:01:41 PDT 2013


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?

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?

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
>
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