Question: set "avg_ins" when using SOAPdenovo
0
gravatar for Yingzi Zhang
2.3 years ago by
Yingzi Zhang60
Jeddah
Yingzi Zhang60 wrote:

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

assembly • 794 views
ADD COMMENTlink modified 2.3 years ago by genomax91k • written 2.3 years ago by Yingzi Zhang60
2
gravatar for genomax
2.3 years ago by
genomax91k
United States
genomax91k wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by genomax91k

Got it. Thank you.

Yingzi

ADD REPLYlink written 2.3 years ago by Yingzi Zhang60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1752 users visited in the last hour