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Old 02-19-2014, 08:57 AM   #1
cnicolet
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Default Nextera exome kit

Hi:
Recently we tested the nextera exome enrichment libe kit. In our analysis pipeline we have a metric that calculates exonic reads, intronic reads, and intergenic reads. Our nextera libes all had about 50% match to the exons. That seemed low, I went back and looked at the same metric from the original illumina kits, those also had only about 50% exonic reads. Does this seem low? It throws a real wrench into coverage calculations
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Old 02-19-2014, 03:04 PM   #2
Bukowski
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What is the on-target specification of Nextera? I don't use Nextera, I use SureSelect, which will generally give ~65% 'on target' reads on variable quality samples, but the Agilent literature claims 70%. For custom capture regions on SureSelect, 50% on target is all you will get, so it depends. Also are you feeding a list of all exons to your coverage metric calculator? Or just the exons in the capture kit?
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Old 02-20-2014, 10:57 AM   #3
cnicolet
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Thanks for your comments. That is an excellent point, I'm sure we are feeding all known exons so that could be a big part of it. I'll know a lot more when we send the sureselect material info through the same pipeline, but it does sound as though those numbers are to be expected. Just looking around on the browser it is clear that are abundant areas of off target seqeuncing.
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