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Pipelines and QC: What is a good mapping percentage?

What is a good mapping percentage?


1 Answer:

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.

Answered on June 5th, 2020 by