Targeted sequencing: Size of target region

[krobison]

I believe it is the size of the region tiled with baits.

In any case, your ability to capture information nearby will be limited by the fragment size used in capture. A lot of capture protocols use relatively short fragments; you'll want to look for one that captures 1Kb or more.

[hazelperry]

We are considering the possibility of doing some targeted sequencing to identify genes under selection, however having read around about it I am a little bit unclear by what is actually meant by the target size. Is this the size of the region we can expect to get sequence data back for or is the the size of the region the baits/probe etc catch/target?

My reason for asking is that we are trying to identify SNP's using RAD at the moment and I hope to be able to get sequence data for ~1Kb either side of my SNP to identify the gene under selection. However if we need to already have sequence data for the target region this wont be possible as our RAD data probably wont be long enough.

Any help/advice would be much appreciated.