SEQanswers - View Single Post - PCR-Free Libraries & Bioinformatic PCR Duplicate detection?

aeonsim · 10-22-2013, 09:52 AM

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.

10-22-2013, 09:52 AM	#1
aeonsim Member Location: Belgium Join Date: Jun 2011 Posts: 45	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.