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Question: Insert size provided by bbmerge
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gravatar for deepti1rao
15 months ago by
deepti1rao • 20
deepti1rao • 20 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 • 558 views
ADD COMMENT • link •
modified 15 months ago by genomax ♦ 62k • written 15 months ago by deepti1rao • 20

The insert-size in paired-end data

ADD REPLY • link modified 15 months ago • written 15 months ago by Sej Modha ♦ 4.0k

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 REPLY • link written 15 months ago by deepti1rao • 20

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

ADD REPLY • link written 15 months ago by genomax ♦ 62k
0
gravatar for genomax
15 months ago by
genomax ♦ 62k
United States
genomax ♦ 62k 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 COMMENT • link modified 15 months ago • written 15 months ago by genomax ♦ 62k

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

ADD REPLY • link written 15 months ago by deepti1rao • 20
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