Variants in mito using Nanopore MinIOn

Question

[dineshgene89]

We did an amplicon sequencing in nanopore for mitochondria, we used Nanopolish to study the variants, but we are not getting any variants after using the software can anyone help us with this. Thanks in advance

[h.mon]

Please explain in more detail your experimental setting and commands used. What is the amplicon target region? Is it a population study, inter-species, or just one individual? And so on.

[colindaven]

Also, how many SNVs can you see directly eye-balling the raw data? If very deep coverage, try downsampling or using the Tablet assembly browser