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.
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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