[khmer] Fwd: Filter Read sequence based on the kmer abundance

[C. Titus Brown]

On Tue, Sep 09, 2014 at 09:32:49AM +0800, Raimi Mohamed Redwan wrote:
> I was trying the khmer to divide the reads based on the coverage as per
> directed in your blog, but I was stuck due to one thing.
> 
> Initially when I always have used Jellyfish to perform kmer counting, and
> then to give me a kmer abundance graph and from here I realized that my
> data have heterozygosity issue due to the presence of double peaks after
> the erroneous error peak.  However, upon doing the abundance plotting using
> the abundance-dist.py and plot-abundance-dist.py, the heterozygote peak is
> now gone and the repeat goes so much higher that what was seen with the
> Jellyfish.
> 
> Attached here is the kmer-abundance plot that I have got from the jellyfish
> and khmer.
> 
> Furthermore, there were two lines in the kmer abundance graph that I
> plotted, what is the second one referring to?

Hi Raimi,

do you know what k-mer size the Jellyfish analysis used?

And you could tell me which commands you were using for khmer? Was it
from this blog post:

http://ivory.idyll.org/blog/2014-slice-reads-by-coverage.html

and did you use abundance-dist, or calc-median-distribution?

thanks,
--titus

> 
> 
> -- 
> Raimi Mohamed Redwan
> Biotechnology Research Institute
> Universiti Malaysia Sabah
> Jalan UMS
> 88400, Sabah
> Malaysia
> 0126707944


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-- 
C. Titus Brown, ctb at msu.edu