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Old 09-28-2015, 11:19 AM   #4
Ingeneious
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Location: Los Angeles, CA

Join Date: Dec 2014
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Quote:
Originally Posted by superduper View Post
I was using one barcode per library.
1. I used the universal 8nt blocking oligo (mix of TS-p5 and TS-p7(8nt))

2. my on-targets were:
single capture; barcoding happens after hyb step (basically XT protocol): 70%
XGen blocking: 58-73%
Inosines instead of barcode location: up to 33%
perfect complement: 45%
random nucleotides: up to 35%

This is for PE37 sequencing. To compare samples where I had run reads longer, I clipped them back to PE37 to have a fair comparison between different conditions.
Your % on-target will increase the longer your read lengths are; I saw PE101 of 82% translate to 69% when I clipped it to PE37.
Did you add any kind of termination to the blocking oligo?
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