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<DIV style="FONT-FAMILY: Times New Roman">Dear Colleague,</DIV>
<DIV style="FONT-FAMILY: Times New Roman">I am doubted with the the set of
cutoff [-C] when using the estimate-genome-size.py program.</DIV>
<DIV style="FONT-FAMILY: Times New Roman">Fist, I use
plot-abundance-dist.py to plot the 17mer spectrum, just as follows(set xlim
& ylim):</DIV>
<DIV style="FONT-FAMILY: Times New Roman"> </DIV>
<DIV style="FONT-FAMILY: Times New Roman"><IMG
src="cid:_Foxmail.0@F924B88E-C4EC-4725-82AE-46E4FE833AFD" width=369
height=298></DIV>
<DIV style="FONT-FAMILY: Times New Roman">From the picture, I assumed those kmer
abundance less than 50X have high frequency and may be derived
from sequencing error. </DIV>
<DIV style="FONT-FAMILY: Times New Roman">So, I set [-C]=50 when using the
estimate-genome-size.py program, and the
Estimated (meta)genome size is: 53602214 bp (our
data is from metagenome and the sequence size is about 5G).</DIV>
<DIV style="FONT-FAMILY: Times New Roman">However, according to your
guidance displayed in the khmer website, I also set [-C]=20 and others
parameter were unchanged when using the estimate-genome-size.py
program,</DIV>
<DIV style="FONT-FAMILY: Times New Roman">but the
Estimated (meta)genome size is: 32765613 bp , what
a big the difference it is!</DIV>
<DIV style="FONT-FAMILY: Times New Roman">So I am confused
about how to choose cutoff [-C]. Hope you can give me some
useful advices. </DIV>
<DIV style="FONT-FAMILY: Times New Roman">Thank you very much!</DIV>
<DIV style="FONT-FAMILY: Times New Roman"> </DIV>
<DIV style="FONT-FAMILY: Times New Roman"> </DIV>
<DIV style="FONT-FAMILY: Times New Roman"> </DIV>
<DIV style="FONT-FAMILY: Times New Roman">
<DIV style="FONT-FAMILY: Times New Roman">Best Wishes</DIV></DIV>
<HR style="WIDTH: 210px; HEIGHT: 1px" align=left color=#b5c4df SIZE=1>
<DIV style="FONT-FAMILY: Times New Roman">Xiao Luo</DIV>
<DIV style="FONT-FAMILY: Times New Roman">BGI-Shenzhen China</DIV></BODY></HTML>