getMT: grab the mitochondrial reads from a BAM and estimate their...
In RamsinghLab/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration
Description
grab the mitochondrial reads from a BAM and estimate their fraction
nb. this could probably be done faster for a list of BAMs but it's not
nb. nb. returns NuMt-depleted mitochondrial GenomicAlignments
Usage
1
Arguments
bam
a BAM filename, which should have an index (else index it)
chrM
what the mitochondrial contig is called. Default is "chrM"
mtGenome
what mitochondrial assembly was used (default is hg19)
plotMAPQ
plot distribution of mitochondrial mapping quality? (FALSE)
RamsinghLab/ATACseeker documentation built on May 8, 2019, 8:05 a.m.
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Description
grab the mitochondrial reads from a BAM and estimate their fraction nb. this could probably be done faster for a list of BAMs but it's not nb. nb. returns NuMt-depleted mitochondrial GenomicAlignments
Usage
1 |
Arguments
bam |
a BAM filename, which should have an index (else index it) |
chrM |
what the mitochondrial contig is called. Default is "chrM" |
mtGenome |
what mitochondrial assembly was used (default is hg19) |
plotMAPQ |
plot distribution of mitochondrial mapping quality? (FALSE) |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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