Hi,
I use bamQC in ATACseqQC to do the quality analysis of our ATAC-Seq data. However, I have some questions below. Could you help me? Many thanks.
Best,
Gary
My questions (1) The meaning of $totalQNAMEs
(2) The meaning of $nonRedundantFraction
(3) The meaning of $MAPQ. Is it mapping quality?
(4) How does ATACseqQC define the low mapping quality in $notPassingQualityControlsRate
(5) The difference between $duplicateRate, $PCRbottleneckCoefficient1, and $PCRbottleneckCoefficient2
bamQC results
> bamfile <- "Bulbul.bam"
> bamfile.label <- sub(".bam","",basename(bamfile))
> bamQC(bamfile, doubleCheckDup = TRUE, mitochondria = "chrM", outPath=NULL)
$totalQNAMEs
[1] 21916261
$duplicateRate
[1] 0.3664853
$mitochondriaRate
[1] 0.1325265
$properPairRate
[1] 0.8650588
$unmappedRate
[1] 0
$hasUnmappedMateRate
[1] 0.009750733
$notPassingQualityControlsRate
[1] 0
$nonRedundantFraction
[1] 0.4259382
$PCRbottleneckCoefficient_1
[1] 0.6878547
$PCRbottleneckCoefficient_2
[1] 3.223372
$MAPQ
Var1 Freq
0 0 1084726
1 1 2871341
11 11 3289972
12 12 104817
14 14 816882
16 16 93679
17 17 501750
18 18 393854
19 19 54317
2 2 885517
21 21 276105
22 22 2311572
24 24 1988876
25 25 157419
28 28 1968735
31 31 157705
32 32 120801
33 33 119436
34 34 123993
35 35 44634
36 36 2199923
37 37 158525
38 38 179100
39 39 203899
40 40 359444
41 41 1728179
42 42 1664509
44 44 19352277
9 9 197263
$idxstats
seqnames seqlength mapped unmapped
1 chr1 148872119 4128800 0
2 chr2 196923045 5417894 0
3 chr3 131294613 3780349 0
4 chr4 91954985 2632716 0
5 chr5 70255457 2138911 0
6 chr6 47769531 1717115 0
7 chr7 48434409 1320034 0
8 chr8 38169314 1097923 0
9 chr9 32183676 909768 0
10 chr10 26112686 759545 0
11 chr11 29734599 926547 0
12 chr12 26924181 784131 0
13 chr13 20766281 587163 0
14 chr14 23539961 695308 0
15 chr15 18414836 502454 0
16 chr16 86149285 2480089 0
17 chr17 18671425 534943 0
18 chr18 16791751 470999 0
19 chr19 13212593 386971 0
20 chr20 20610846 610399 0
21 chr21 10574128 301684 0
22 chr22 7051356 305518 0
23 chr23 8322055 267565 0
24 chr24 9986730 340468 0
25 chr25 2816729 118446 0
26 chr26 8520532 272092 0
27 chr27 8282467 251498 0
28 chr28 7839907 262123 0
29 chr29 1612305 44851 0
30 chr30 23086460 897442 0
31 chr31 1266911 40603 0
32 chr32 81982468 2672024 0
33 chrM 17011 5752877 0
Hi Jianhong,
Thanks a lot. May I have an additional question? Using ENCODE's terms and definitions for the ATAC-Seq library complexity, I don't understand why (1) my bottlenecking level is "Severe" based on my PBC1 value (0.6878547 < 0.7), but (2) my bottlenecking level is "None" base on my PCB2 value (3.223372 > 3). Could you help me? Many thanks.
Best,
Gary