Simulating human mitochondrial reads from reference mitochondrial genome

[Rohit-Satyam]

Hi Developers!!

Thanks for making such a straightforward tool for simulation. I wish to simulate reads from Mitochondrial genome reference fasta but I am confused about what distribution should I choose from 4 options that you provide. In terms of coverage the mitochondrial genomes attract a lot of reads and since it's small it gets uniformly covered I think. I am confused your coverage option takes care of Horizontal Coverage or Vertical coverage??

If it's vertical coverage, does it mean that simulated reads preferentially comes from one region of the reference genome (say from either 5' end or 3' end).

Besides, what's the difference between behavior of Abundance and Coverage parameter?

[HadrienG]

Hi!

Sorry for the very slow reponse time. Are you simulating from a mixture of mitochondria or from a single reference genome?

[Rohit-Satyam]

It was only from single reference genome.