Question: Near Target Reads In Whole Exome Data
0
gravatar for User6891
6.9 years ago by
User6891280
Europe
User6891280 wrote:

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?

read exome-sequencing • 1.4k views
ADD COMMENTlink modified 6.9 years ago by skymningen330 • written 6.9 years ago by User6891280
1
gravatar for skymningen
6.9 years ago by
skymningen330
Germany
skymningen330 wrote:

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.

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by skymningen330

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

ADD REPLYlink written 6.9 years ago by User6891280
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