Near Target Reads In Whole Exome Data

Question

[User6891]

Hi,

Sometimes you see that besides calculating the coverage in target regions, people also look at near-target & off-target regions.

What would you consider as near-target regions for whole-exome data? I thought of 50bp before and after the start/end of the exon, but I'm not sure if this is a good boundary. Does someone have experience with this?

Answer 1

[skymningen]

That depends on the target capture method. For example, for Agilent SureSelect, you can capture up to 200 bp next to the target (at least they state that, I haven't had the chance to check yet). So, preferably to determine the amount of near-target region that you need to consider, best check the specifications of the target capture.

[User6891]

Thanks for the tip. I'm using Roche Nimblegen v2 of v3 by the way