Table 1 Triform parameters
From: The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
Parameter | Description |
|---|---|
w | read width, symmetrically extended to a fixed value (default 100 bp) |
δ | fixed spacing between central and flanking locations (must be > w, default 150 bp) |
r | actual ratio between control and ChIP-Seq library sizes |
min.z | fixed minimum upper-tail z-value (default corresponds to standard normal p = 0.1) |
min.n | fixed minimum number of bp (peak width) in peak-like region (default 10 bp) |
min.er | fixed minimum local enrichment ratio (default 3/8 quantile of the enrichment ratio) |
min.lag | fixed minimum inter-strand lag between peak coverage distributions (default 10 bp) |