View source: R/00.get_GCandMappability.R
mapComp | R Documentation |
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
mapComp(mi)
mi |
A numeric vector of mappability along per chromosome/scaffold |
Calculate weights for mappability-base coverage correction
A numeric vector of weights for mappability-based coverage correction
Jianhong Ou
Derrien et al. Fast computation and applications of genome mappability. PLoS One. 2012;7(1):e30377. doi: 10.1371/journal.pone.0030377.
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