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Hi, I am trying to run bamQC function of ATACseqQC. I am running the following command but getting an error after waiting an hour. Can somebody please advise how to handle it?
**Code**: bamQC("Aligned_S2.bam", index="Aligned_S2.bam.bai", mitochondria = "chrM", doubleCheckDup = FALSE, outPath = sub(".bam", ".clean.bam", basename(Aligned_S2)))
**Error:**
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'path' in selecting a method for function 'basename': object 'Aligned_S2' not found
Calls: bamQC ... sub -> is.factor -> basename -> .handleSimpleError -> h
Execution halted
Thank you for trying ATACseqQC to analyze your data. Could you let me know what is 'Aligned_S2' in your code
basename(Aligned_S2)
?