I have searched for the answer but I still need more clear explanation to understand the concept.
we need to filter out exons that have extremely low coverage (median read depth across all samples less than 20, which mostly reflect capture failure).
As I know, the concept of coverage depth is different from read depth... coverage depth simply means how much each segmentation is covered by the sequencing platform. While read depth means how many times a segmentation has been read. (please correct me if I'm wrong).
now my question is how can "extremely low coverage" be defined as "median read depth across all samples less than 20"?
could someone give me a clear explanation of "median" read depth?
Thank you so much