Lenght of fragment for Illimina TruSeq sample prep

[barbarian]

Hello,

I just want to know. During the TruSeq v2 sample preparation workflow, the first step is purify and fragment mRNA. My question is how long this fragmentation method will produce? Is the length same or different for each mRNA? Is there any way to know how long per fragment as a result of this procedure from FASTA/FASTQ/SAM file? Thank you for your answer.

[nucacidhunter]

The length of fragments depends on exposure time and you can find it in user guide. The average and range of fragment size distribution can be estimated by running prepped library on Bioanalyzer or by mapping paired end reads.

[pmiguel]

The trick to getting the minimum insert length you want is to use shorter fragmentation times -- but even more importantly -- you drop the concentration of Ampure used to clean the reaction up.

--
Phillip