Question: bowtie2 mixed vs discordant
0
gravatar for donkirkby
3.0 years ago by
donkirkby0
Canada
donkirkby0 wrote:

I'm using bowtie2 to map a FASTQ file of reads from an Illumina MiSeq to some reference sequences, and I'm trying to understand the difference between discordant and mixed pairs.

In the bowtie2 manual, it describes discordant pairs as having the two reads in unexpected relative positions. For example, the reverse read earlier than the forward read, or the two reads too far apart.

The manual just says that mixed mode will try to map the individual reads separately if they fail to map as a pair. However, when I compare a pair that will only map in mixed mode with a pair that maps discordantly, I can't see any difference. They both just have a base or two extra on the reverse read that extends past the start of the forward read.

What stops a pair of reads from mapping together?

I'm using the --local option, if that's important, and I do see soft clipping.

next-gen alignment • 1.1k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by donkirkby0
0
gravatar for donkirkby
3.0 years ago by
donkirkby0
Canada
donkirkby0 wrote:

The manual describes this clearly, I just hadn't noticed it: "To declare that a pair aligns discordantly, Bowtie 2 requires that both mates align uniquely. This is a conservative threshold, but this is often desirable when seeking structural variants."

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by donkirkby0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1638 users visited in the last hour