set "avg_ins" when using SOAPdenovo

Question

[Yingzi Zhang]

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

Answer 1

[GenoMax]

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

[Yingzi Zhang]

Got it. Thank you.

Yingzi