Command: normalize

Calculate normalized rates of events in a qBED file

usage: blockify normalize [-h] -i INPUT [--prior PRIOR | --p0 P0]
                          [--method {OP,PELT}] [-r REGIONS] [-o OUTPUT]
                          [-k LIBRARYFACTOR] [-l LENGTHFACTOR]

Named Arguments

-i, --input

Input file

--prior

Explicit prior on the number of blocks (not recommended for general use)

--p0

Empirical prior based on a specified false-positive rate; must be between 0 and 1 (default: 0.05)

--method

Possible choices: OP, PELT

Segment using the optimal partitioning (OP) or pruned exact linear time (PELT) algorithm (default: “PELT”)

-r, --regions

Regions over which to normalize event counts; should be supplied as a BED file. If not provided, the input file will be segmented using Bayesian blocks.

-o, --output

Output file (bedGraph format); default: stdout

-k, --libraryFactor

Normalization factor for library size (default: 1000000)

-l, --lengthFactor

Normalization factor for the length of regions; used to calculate scaled rates of events per interval (default: None)