diff --git a/README.md b/README.md index 6a96fc1f3e08297afbdf2524cb2a2d3adee43113..85c54379d43822787160f31c6b4254b1517b7e2a 100644 --- a/README.md +++ b/README.md @@ -107,7 +107,7 @@ With this method, we retain the interesting properties of [Hu et al.](https://do ### Genome coverage density -To compute the coverage density $X_y(t)$ with $X \in \left{IP, WCE\right}$ and $y \in \left{c, x\right}$ we count the number of read $r(t)$ overlapping with position $t$. +To compute the coverage density $X_y(t)$ with $X \in \left[IP, WCE\right]$ and $y \in \left[c, x\right]$ we count the number of read $r(t)$ overlapping with position $t$. For properly paired reads (with a mate read on the same chromosome and with a starting position ending after the end of the read) we also count a density of 1 between the end of the first reads and the start of his mate read $g(t)$. $X_y(t) = r(t) + g(t)$. Some fragment can be artificially long, therefore, we compute a robust mean $\mu$ of the gap size, between two reads of a pair, by removing the 0.1 upper and lower value of fragment length. Fragment that has a size higher than $\phi^{-1}(0.95, /mu, 1.0)$ are set to end at the $\phi^{-1}(0.95, /mu, 1.0)$ value, with $\phi()$ the Normal CDF function.