Hi,
I did some alignment of DNA libraries using bowtie2.
I tested with and without -k option.
Without -k options (-k 10 in this example), MAPQ ranged between 0 and 42 .
MAPQ Freq
1 0 29201
2 1 584134
3 2 6504
4 3 5377
5 4 251
6 5 27
7 6 144827
8 7 21386
9 8 6020
10 11 1481
11 12 2500
12 14 182
13 15 575
14 16 82
15 17 114
16 18 160
17 21 99
18 22 339
19 23 6940
20 24 7299
21 25 43
22 26 91
23 27 84
24 30 1305
25 31 266
26 32 269
27 34 456
28 35 790
29 36 22
30 37 8
31 38 41
32 39 341
33 40 13110
34 42 951540
With -k 10 : MAPQ ranged between 0 and 255
MAPQ Freq
1 0 40438
2 1 2023162
3 2 41425
4 3 3822
5 4 820
6 5 239
7 6 717882
8 7 29605
9 11 25711
10 12 1922
11 14 1548
12 15 4672
13 16 972
14 17 578
15 18 304
16 21 548
17 22 1554
18 25 257
19 26 661
20 27 26
21 30 818
22 31 1068
23 32 1327
24 34 1580
25 35 3890
26 36 78
27 37 35
28 38 80
29 39 350
30 255 430525
When I take the MAPQ 255 reads a look at their corresponding MAPQ in the "without -k" alignment I found MAPQ between 0 and 42 (most of them are 42). I do not understand why MAPQ will be differnet in -k mode ? I expected to have same MAPQ as -k mode will only output up to 10 (if -k 10) valid alignment per reads (stop me if I'm wrong ?).
MAPQ Freq
1 0 4053
2 1 29681
3 2 157
4 3 520
5 4 8
6 5 4
7 6 2420
8 7 73
9 8 773
10 11 72
11 12 14
12 14 4
13 15 27
14 16 4
15 21 1
16 22 12
17 23 1019
18 24 1142
19 26 4
20 30 72
21 31 17
22 32 1
23 34 2
24 39 2
25 40 3021
26 42 387953
FYI : bowtie2-2.2.9