Got it. Thank you.
Yingzi
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set "avg_ins" when using SOAPdenovo
Hi, all:
I am using SOAPdenovo. When preparing config file, I need to set avg_ins. I know it means the average insert size of my library. I did insert size estimation.
It reported like this:
insert size (inside of regions) mean 57,532.59 standard deviation 2,318,948.24 P25/median/p75 461/469/478
So I think I should set avg_ins = 57,533, but examples on the internet usually set it as avg_ins = 200. Is my understanding wrong? Any suggestions please? Thank you.
ps. my data are 100bp x 2 reads
Yingzi
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GenoMax
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Yingzi Zhang
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Yingzi Zhang
1 answer
That is incorrect. For Illumina libraries insert sizes should be in ~350-500 bp range. So these numbers seem correct: P25/median/p75 461/469/478
You can estimate insert sizes using BBMap suite like this: C: Target fragment size versus final insert size
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