search

jianhong / ATACseqQC

ATAC-seq Quality Control
https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html
23 stars 12 forks source link

Question about bamQC #44

Open etiennedanis opened 3 years ago

etiennedanis commented 3 years ago

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 commented 2 years ago

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