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

[Raimi Mohamed Redwan]

Hi,

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 reads.kh reads.fa |
abundance-dist.py -s reads.kh reads.fa reads.dist  |
 ./plot-abundance-dist.py reads.dist reads-dist.png ).

Thank You

On Fri, Sep 12, 2014 at 7:05 PM, C. Titus Brown <ctb at msu.edu> wrote:

> 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
>
>
> > _______________________________________________
> > khmer mailing list
> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer
>
>
> --
> C. Titus Brown, ctb at msu.edu
>



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



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