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 <a href="http://khmer.readthedocs.org/en/latest/scripts.html">http://khmer.readthedocs.org/en/latest/scripts.html</a>. Can anyone help?<div>
<br></div><div>Thanks in advance.</div><div>Rajat<br><br><div class="gmail_quote">On Thu, Jun 20, 2013 at 9:27 AM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5">On Thu, Jun 20, 2013 at 08:31:52AM -0400, Rajat wrote:<br>
> Hi Prof ,<br>
> I tried to follow the example at<br>
> <a href="http://khmer.readthedocs.org/en/latest/ktable.html" target="_blank">http://khmer.readthedocs.org/en/latest/ktable.html</a> to extract kmers using<br>
> khmer. It works fine for small values of k (<=15) but exits without any<br>
> output as soon as I make k>=16. In<br>
> <a href="http://khmer.readthedocs.org/en/latest/ktable.html" target="_blank">http://khmer.readthedocs.org/en/latest/ktable.html</a> they mention that it<br>
> does not work for k>12 on their machines. However, it is mentioned in<br>
> <a href="http://khmer.readthedocs.org/en/latest/introduction.html" target="_blank">http://khmer.readthedocs.org/en/latest/introduction.html</a> that khmer can<br>
> count kmers for k<=32. Could you point me to some examples that I can<br>
> follow to count 31 mers with khmer?<br>
<br>
</div></div>Hi Rajat,<br>
<br>
please see this recent thread on the khmer mailing list:<br>
<br>
<a href="http://lists.idyll.org/pipermail/khmer/2013-June/thread.html#start" target="_blank">http://lists.idyll.org/pipermail/khmer/2013-June/thread.html#start</a><br>
<br>
Briefly, ktable does the "dumb thing" and allocates 4**k bytes of memory,<br>
which only works up to ~k=15 on many computers. The counting hash data<br>
structure will count for much larger k.<br>
<br>
You can also take a look at this IPython Notebook:<br>
<br>
<a href="http://nbviewer.ipython.org/urls/raw.github.com/ngs-docs/ngs-notebooks/master/ngs-5x-kmer-abundance-distributions-2013.ipynb" target="_blank">http://nbviewer.ipython.org/urls/raw.github.com/ngs-docs/ngs-notebooks/master/ngs-5x-kmer-abundance-distributions-2013.ipynb</a><br>
<br>
for information on getting k-mer abundance distributions.<br>
<br>
best,<br>
--titus<br>
<span class="HOEnZb"><font color="#888888">--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu">ctb@msu.edu</a><br>
</font></span></blockquote></div><br></div>