Hi all,

I am new person in NGS analysis. I am using ATACseqQC as suggest in the tutorial pubblished recently April 2020 to asses my ATAC-seq data.

In terestingly I found that when I use the following code across all my BAM files, it returns always with the same tags.

possibleTag <- combn(LETTERS, 2)
possibleTag <- c(paste0(possibleTag[1, ], possibleTag[2, ]),
                 paste0(possibleTag[2, ], possibleTag[1, ]))
library(Rsamtools)
bamTop100 <- scanBam(BamFile(bamfile, yieldSize = 100),
                     param = ScanBamParam(tag=possibleTag))[[1]]$tag
tags <- names(bamTop100)[lengths(bamTop100) == 100]
tags

[1] "PG" "YT"

 [1] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
  [6] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [11] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [16] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [21] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [26] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [31] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [36] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [41] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [46] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [51] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [56] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [61] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [66] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [71] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [76] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [81] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [86] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [91] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
 [96] "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates" "MarkDuplicates"
>

Any suggestions?

I really appreciate any help. Thanks a lot