Haploid determination

[Pikayy]

Hi,

Is there any chance nQuire can be adapted to detect haploid species? I am working with a haploid-diploid organism that the females are diploid and males a re haploid.

Best

[clwgg]

Hi,

with the current model, it is unfortunately not possible to explicitly model haploids. However, I've implemented the denoise subcommand, in part, to be able to investigate haploids. The idea there is that haploids will approximately look like uniform noise - so haploids will have a substantially higher fraction of data removed during denoising (this fraction is output after the denoise command is run). It might be worth to play with the denoising a little and see if there is a bimodal distribution in the amount denoising removes when distinguishing haploids from diploids.

[chiu-shenpo]

How to know whether the removed data is caused by sequencing error NGS reads that mapped to genome or its actual haploid???