#267 bowtie2 overlapping pairs

open
nobody
bowtie (175)
5
2013-01-20
2013-01-20
Jorja Henikoff
No

Hello, We're comparing bowtie2 with Novoalign for short paired-end reads and we can't make sense of some of the
results where the 2 reads seem to overlap, we are very interested in these pairs. Here's an example:

bowtie2 --local --very-sensitive-local --no-discordant --no-contain -I 10 -X 700
(so overlaps allowed)
What are the start and end positions of the insert?
Why was read1 mapped on the forward strand (FLAG=99) and to the left
of read2 (5220636 < 5220638) but is called the rightmost mate (TLEN=-27)?

1 DH1DQQN1:240:C0VJ4ACXX:1:1101:13044:11671 DH1DQQN1:240:C0VJ4ACXX:1:1101:13044:11671
2 99 147
3 3L 3L
4 5220636 5220638
5 0 0
6 16M8S 3S21M
7 = =
8 5220638 5220636
9 -27 27
10 TGTGTGTGTGTGTGTGCATCTAGA TCTTGTGTGTGTGTGTGTGCATCT
11 1:4AA=CC<<<CAEE<<ACFF< 9GBC?BFGF;GDDHHFBDDB1@@@
12 AS:i:32 AS:i:42
13 XS:i:42 XS:i:42
14 XN:i:0 XN:i:0
15 XM:i:0 XM:i:0
16 XO:i:0 XO:i:0
17 XG:i:0 XG:i:0
18 NM:i:0 NM:i:0
19 MD:Z:16 MD:Z:21
20 YS:i:42 YS:i:32
21 YT:Z:CP YT:Z:CP

Discussion