How to use binoSNP to detect low frequency SNPs in eukaryotic RNA-seq data?

[janstrauss1]

Hi there,

I'd like to use binoSNP to detect subpopulations in my eukaryotic RNA-seq data and tried to set it up accordingly by supplying my own list of intervals, mutation table and (multiple scaffold/chromosome) reference sequence.

Although binoSNP appears to run smoothly on the supplied files, the output is empty.
I'm currently don't know where the issue is but wondered if you could provide an example bam.file to test that binoSNP runs smoothly in my environment?

Also, I'd appreciate any tips on how to use binoSNP on eukaryotic data sets.

Many thanks in advance for your help!

[vdreyer]

Hi,
sorry for the late response. Unfortunately, we are working with procaryotic data sets, only, so that I don't have useful tips. However, I think the whole calculation is not usable in an eucaryotic environment, as it is specified for procaryotic DNA.
Greetings,
Viola