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Insert Size And Fragment Size ?

Hi,

Simple question but I'm a little bit confused due to different description I read. So what is the difference between insert size and fragment size in DNA-Seq ( or RNA-Seq ) ?

Thanks

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written by Nicolas Rosewick Nicolas Rosewick

3 answers

See the above figure ( from What is the difference between a Read and a Fragment in RNA-seq? )

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written by -_- -_-

@-_- Link is broken. Btw, thanks for the picture, it tells enough!

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written by manetsus • manetsus

Thanks. Does the insert size calculation require alignment of both Read 1 and Read 2 to reference genome first?

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written by xiaoleiusc xiaoleiusc

Yes. If you have paired-end reads you should always align them at the same time e.g. bwa mem genome.fa R1.fastq.gz R2.fastq.gz > align.sam

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written by Nicolas Rosewick Nicolas Rosewick

I guess that depends on the person who is using it.

I would say (for Illumina): Fragment size is the size of the actual fragments that you put into the sequencer (including adapter sequences). Insert size is the length of the DNA (or RNA) that you want to sequence and that is "inserted" between the adapters (so adapters excluded).

BUT fragment size could also be the size of the fragments after shearing which would be insert size by my definition above.

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updated by lieven.sterck lieven.sterck • written by lelle lelle

The insertsize dependent on sequencing platform.

Insert_size = the sequence betwwn adapters

Fragment_size= Insert_size + Adapters

The link will clarify your ambuguity.

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written by murali murali

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