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Old 05-01-2014, 11:02 AM   #1
ASL
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Location: Virginia, USA

Join Date: Apr 2013
Posts: 5
Question Illumina TruSeq adaptor issue?

Hello everyone,

I am using the Illumina TruSeq ChIP Sample Prep kit (Set A adaptors) to generate my ChIP-Seq libraries. One of the indexes (#19) gives me libraries that look okay on the Bioanalyzer, but the number of unique reads are consistently lower as compared with libraries made with other indexes. Illumina tech support tells me that while "different indexes may have different clustering and amplification efficiency" they do not "necessarily see this as consistent trends". I'd believe them if it were just that index from my kit. However, another lab in our department with a different TruSeq kit (working with a different organism and target) has this same issue with that index. Has anyone else had an issue? Are there indexes that are better avoided?

Thanks!
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