Insert Size And Fragment Size ?

Question

[Nicolas Rosewick]

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

Answer 1

[-_-]

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

[manetsus]

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

[xiaoleiusc]

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

[Nicolas Rosewick]

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

Answer 2

[lelle]

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.

Answer 3

[murali]

The insertsize dependent on sequencing platform.

Insert_size = the sequence betwwn adapters

Fragment_size= Insert_size + Adapters

The link will clarify your ambuguity.