Question: Insert size provided by bbmerge
0
gravatar for deepti1rao
2.6 years ago by
deepti1rao30
deepti1rao30 wrote:

My illumina paired end reads are 150 bases long.

I ran bbmerge to check the insert size. Following is the link for the screen shot.

https://ibb.co/gpySf6

How can I have an avg insert size of 243 and a maximum of 291 when my reads themselves are 300 (2*150)? Does insert size here mean the inner distance (distance between R1 and R2)? I'm aware that there's ambiguity in the definition of insert size.

So, shall I consider the avg insert size to be 243 + 150 + 150 = 540 ??

insert bbmerge • 1.1k views
ADD COMMENTlink modified 2.6 years ago by genomax85k • written 2.6 years ago by deepti1rao30

The insert-size in paired-end data

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Sej Modha4.7k

I went through this Sej.I want to know how I can have such small insert sizes if I have reads which are 150 each.

ADD REPLYlink written 2.6 years ago by deepti1rao30

Insert sizes are a characteristic of your libraries and have nothing to do with read lengths.

ADD REPLYlink written 2.6 years ago by genomax85k
0
gravatar for genomax
2.6 years ago by
genomax85k
United States
genomax85k wrote:

See the explanation in this thread: BBMap and BBmerge insert sizs

|------------------------------>100 bp|    R1 - 150 bp
|-------------------------------------|    Fragment 250 bp
|100 bp<------------------------------|    R2 - 150 bp
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by genomax85k

So there's an overlap of 50 bp between the mates.

ADD REPLYlink written 2.6 years ago by deepti1rao30
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