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Old 11-06-2019, 11:14 AM   #9
SNPsaurus
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Originally Posted by samd View Post
@SNPsaurus

I have not done that. I know that is much more accurate we just don't exactly have the capabilities in my lab. However, I can use another lab's qPCR machine I would just have to learn the protocol and all. Would this likely help get much better runs?
Sam
After seeing the updates it probably wouldn't help much. Some library preps can have a high percentage of non-functional DNA fragments but a PCR amplicon should be pretty reliable. And if you are getting 25 million raw reads and then just 11 million the issue is somewhere in the demultiplexing perhaps? Have you looked at the undetermined fastq file and looked for index sequences to see if they have Ns or are not present in the index sequence list?
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