[khmer] counting 31-mers with khmer

Rajat rajatshuvro at gmail.com
Thu Jun 20 11:25:58 PDT 2013


Thanks. I got it running with load-into-counting.py. However, I want to
print out the k-mers with frequencies in a file. I don't see any example
for doing that in http://khmer.readthedocs.org/en/latest/scripts.html. Can
anyone help?

Thanks in advance.
Rajat

On Thu, Jun 20, 2013 at 9:27 AM, C. Titus Brown <ctb at msu.edu> wrote:

> On Thu, Jun 20, 2013 at 08:31:52AM -0400, Rajat wrote:
> > Hi Prof ,
> > I tried to follow the example at
> > http://khmer.readthedocs.org/en/latest/ktable.html to extract kmers
> using
> > khmer. It works fine for small values of k (<=15) but exits without any
> > output as soon as I make k>=16. In
> > http://khmer.readthedocs.org/en/latest/ktable.html they mention that it
> > does not work for k>12 on their machines. However, it is mentioned in
> > http://khmer.readthedocs.org/en/latest/introduction.html that khmer can
> > count kmers for k<=32. Could you point me to some examples that I can
> > follow to count 31 mers with khmer?
>
> Hi Rajat,
>
> please see this recent thread on the khmer mailing list:
>
> http://lists.idyll.org/pipermail/khmer/2013-June/thread.html#start
>
> Briefly, ktable does the "dumb thing" and allocates 4**k bytes of memory,
> which only works up to ~k=15 on many computers.  The counting hash data
> structure will count for much larger k.
>
> You can also take a look at this IPython Notebook:
>
>
> http://nbviewer.ipython.org/urls/raw.github.com/ngs-docs/ngs-notebooks/master/ngs-5x-kmer-abundance-distributions-2013.ipynb
>
> for information on getting k-mer abundance distributions.
>
> best,
> --titus
> --
> C. Titus Brown, ctb at msu.edu
>
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