Question about bamQC

[etiennedanis]

Hi Jianhong,

Thank you again so much for creating ATACseqQC!

To get the report of all the QC metrics with bamQC, it looks like I should use:
bamQC(bamFile, outPath = NULL)

To get the bam files cleaned up, it looks like I should use:
bamQC(bamfile,
index = bamfile,
mitochondria = "chrM",
outPath = sub(".bam", ".clean.bam", basename(bamfile)),
doubleCheckDup = FALSE)

Am I correct?
Is there a way to get both the QC metrics and the bam files cleaned up at the same time?

Thank you very much in advance.
Best,
Etienne

[jianhong]

Sorry for the late reply.
I think this is correct and same as it shown in the documentation.