Question: Using long reads to find a combination of mutations
0
gravatar for eayasi
3.3 years ago by
eayasi0
eayasi0 wrote:

Does anyone know of a way to quantify multiple connected mutations on single reads? I am trying to use my nanopore reads to see if specific combinations stand out. The reads are pretty noisy and doing it by hand seems tedious!

ADD COMMENTlink modified 3.3 years ago by colindaven2.4k • written 3.3 years ago by eayasi0

So you want to phase your variants?

I think WhatsHap does what you need.

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k

This is on the right track of what I want to do. I forgot to mention I am not working with a diploid genome, but a plasmid library. I am not sure if this program will give me the data I am looking for, but I will test it out.

ADD REPLYlink written 3.3 years ago by eayasi0
0
gravatar for colindaven
3.3 years ago by
colindaven2.4k
Hannover Medical School
colindaven2.4k wrote:

Whatshap or Phaser https://github.com/secastel/phaser are on the right track here.

However I think these problems a) only work with maximal diploid ploidy and b) will struggle with nanopore reads.

I would first correct the reads by running canu on them, then use the resultant corrected fastq for further analysis.

Good luck

ADD COMMENTlink written 3.3 years ago by colindaven2.4k
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