bamQC {ATACseqQC} | R Documentation |
Check the mapping rate, PCR duplication rate, and mitochondria reads contamination.
bamQC( bamfile, index = bamfile, mitochondria = "chrM", outPath = sub(".bam", ".clean.bam", basename(bamfile)), doubleCheckDup = FALSE )
bamfile |
character(1). File name of bam. |
index |
character(1). File name of index file. |
mitochondria |
character(1). Sequence name of mitochondria. |
outPath |
character(1). File name of cleaned bam. |
doubleCheckDup |
logical(1). Double check duplicates or not if there is no tags for that. |
A list of quality summary.
Jianhong Ou
bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC") bamQC(bamfile, outPath=NULL)