<div dir="ltr"><div class="gmail_quote"><div dir="ltr">Hi, <div><br></div><div>I used for both the kmer of 17. I followed the one in blog you directed (i.e. load-into-counting.py -x 1e8 -k 17 <a href="http://reads.kh" target="_blank">reads.kh</a> reads.fa | abundance-dist.py -s <a href="http://reads.kh" target="_blank">reads.kh</a> reads.fa reads.dist | ./plot-abundance-dist.py reads.dist reads-dist.png ). </div><div><br></div><div>Thank You</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 12, 2014 at 7:05 PM, 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"><span>On Tue, Sep 09, 2014 at 09:32:49AM +0800, Raimi Mohamed Redwan wrote:<br>
> I was trying the khmer to divide the reads based on the coverage as per<br>
> directed in your blog, but I was stuck due to one thing.<br>
><br>
> Initially when I always have used Jellyfish to perform kmer counting, and<br>
> then to give me a kmer abundance graph and from here I realized that my<br>
> data have heterozygosity issue due to the presence of double peaks after<br>
> the erroneous error peak. However, upon doing the abundance plotting using<br>
> the abundance-dist.py and plot-abundance-dist.py, the heterozygote peak is<br>
> now gone and the repeat goes so much higher that what was seen with the<br>
> Jellyfish.<br>
><br>
> Attached here is the kmer-abundance plot that I have got from the jellyfish<br>
> and khmer.<br>
><br>
> Furthermore, there were two lines in the kmer abundance graph that I<br>
> plotted, what is the second one referring to?<br>
<br>
</span>Hi Raimi,<br>
<br>
do you know what k-mer size the Jellyfish analysis used?<br>
<br>
And you could tell me which commands you were using for khmer? Was it<br>
from this blog post:<br>
<br>
<a href="http://ivory.idyll.org/blog/2014-slice-reads-by-coverage.html" target="_blank">http://ivory.idyll.org/blog/2014-slice-reads-by-coverage.html</a><br>
<br>
and did you use abundance-dist, or calc-median-distribution?<br>
<br>
thanks,<br>
--titus<br>
<span><br>
><br>
><br>
> --<br>
> Raimi Mohamed Redwan<br>
> Biotechnology Research Institute<br>
> Universiti Malaysia Sabah<br>
> Jalan UMS<br>
> 88400, Sabah<br>
> Malaysia<br>
> 0126707944<br>
<br>
<br>
</span>> _______________________________________________<br>
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<div><div><br>
<br>
--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(136,136,136)"><div>Raimi Mohamed Redwan</div><div><div>Biotechnology Research Institute</div><div>Universiti Malaysia Sabah</div><div>Jalan UMS</div><div>88400, Sabah</div><div>Malaysia</div></div><div>0126707944</div></span></div>
</div>
</div></div></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(136,136,136)"><div>Raimi Mohamed Redwan</div><div><div>Biotechnology Research Institute</div><div>Universiti Malaysia Sabah</div><div>Jalan UMS</div><div>88400, Sabah</div><div>Malaysia</div></div><div>0126707944</div></span></div>
</div>