QuestionsCategory: ChIP-Seq Data AnalysisPipelines and QC: What is a good mapping percentage? Staff asked 3 years ago

What is a good mapping percentage?

1 Answers Staff answered 3 years ago

If adapters and sequencing primers are properly trimmed off followed by purging of reads aligning to the blacklisted region, one can expect > 80-85% reads to align to the genome. This number is also assuming that there is no significant contaminant in your sample. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.