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Old 06-18-2014, 06:10 PM   #14
woodydon
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Location: https://www.researchgate.net/profile/Woody_Lin

Join Date: Jan 2010
Posts: 52
Wink

Quote:
Originally Posted by Brian Bushnell View Post
Woody,

Did you try error-correcting and using the 'vloose' setting? Both of those can substantially improve the merge rate.

If you want to see what the actual, unbiased insert size distribution of your data, then you can generate a histogram by mapping:

bbmap.sh in1=read1.fq in2=read2.fq ref=reference.fa ihist=ihist.txt nodisk

Then plot a graph of 'ihist.txt', so you can see how many reads should be expected to assemble.
Great. That's an neat option.
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