Guideline of size selection? Suggestions of using NEBnext kit?

[liumangmang]

Hi,
I'm new to Illumina sequencing. Is there any guideline for size selection step in terms of how many bp are the most often used in Illumina pair end sequencing? 200-300bp?
Will this step bring in bias because fragments of other length are eliminated?

I plan to use NEBnext Ultra DNA library prep kit. Any tricks or suggestions about using this kit and AMPure XP beads for size selection?

Thanks a lot

[jwfoley]

At least for TruSeq, the adapter sequences are a little over 100 bases, so if you select 200-300 bases, you'll only have 100-200 bp inserts. That means if you read 2x100 bases, your reads will usually overlap and you'll waste a large fraction of your sequencing. (Unless you want to be really confident about the base calls in the middle by sequencing them twice.)

So make sure your fragments are going to be big enough for the read length you're planning on. But try not to overshoot too much, because the larger your library is, the more biased it's going to be to small amplicons (especially adapter dimers).