Hello,
I mapped my RNA-seq files (paired end stranded libraries) using RNA-STAR (splice-aware mapping: I provided the Ensemble reference FASTA file as well as the gtf file), and then the output BAM file was used for 'Mark Duplicates.'I then did MultiQC on ‘Mark Duplicate metrics’ and the picard deduplication plots indicated that most of my samples had upto 70% of duplicate pairs non optical, while ‘duplicate pairs optical’ is only 0.1%.
Q1. Could someone please let me know what does non-optical duplicates in PICARD mean?
Many thanks,
GG