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Old 10-22-2013, 08:52 AM   #1
aeonsim
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Location: Belgium

Join Date: Jun 2011
Posts: 45
Default PCR-Free Libraries & Bioinformatic PCR Duplicate detection?

Does any one have any thoughts or experience with regards to the Bioinformatics pipeline for Illumina PCR-Free libraries?

Especially with regards to the need to run Picards MarkDuplicates or some other PCR duplicate detection tool?

As we've started a large sequencing project using the PCR-Free libraries and having run Markduplicates over the initial test lane of sequence it's reporting a PCR-duplicate rate of between 0.004-0.006. Some of which it claims are Optical Duplicates and the rest (2.5x the Optical numbers) it claims are Library duplicates. However considering the kit & protocol was one of the PCR-Free ones I'm wondering if these are actual duplicates or misidentification by Markduplicates (potentially reads from repetitive regions).

Any thoughts would be greatly appreciated.
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