mapComp: Calculate weights for mappability-base coverage correction

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Calculate weights for mappability-base coverage correction

Description

mappability is calculated by using GEM with the following command lines: PATH=$PATH:~/bin/GEM-binaries-Linux-x86_64-core_i3-20130406-045632/bin ./gem-indexer -i genome.fa -o mm10.index.gem ./gem-mappability -I mm10.index.gem.gem -l 100 -o mm10.mappability ./gem-2-wig -I mm10.index.gem.gem -i mm10.mappability -o mm10.mappability.wig

Usage

mapComp(mi)

Arguments

mi	A numeric vector of mappability along per chromosome/scaffold

Details

Calculate weights for mappability-base coverage correction

Value

A numeric vector of weights for mappability-based coverage correction

Author(s)

Jianhong Ou

References

Derrien et al. Fast computation and applications of genome mappability. PLoS One. 2012;7(1):e30377. doi: 10.1371/journal.pone.0030377.

jianhong/InPAS documentation built on Oct. 27, 2023, 2:13 p.m.