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

Raimi Mohamed Redwan raimiredwan at gmail.com
Mon Sep 8 18:32:49 PDT 2014


Hi,

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?


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