We use two different strategies for duplicate removal depending on where the input fastq files are single-end(SE) or paired-end(PE). For PE reads, Picard Tools MarkDuplicate is used to find read pairs with the exact same start and end mapping coordinates duplicates are then marked for removal. For SE reads, the MACS2 filterdup command is used to remove duplicates (partial removal). – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
Please login to submit your answer