[mamba-help] Question for analysis of ASE using mamba

[Kyu-Tae K. <thi...@gm...>]

Dear Dr.Rivas,

It was great to know how genetic variants affect transcriptional dynamics
from your substantial efforts with GTEx consortium that have been reported
in Science, 2015.

I'm Kyu-Tae Kim from Samsung Medical Center (Korea) and studying cancer
genomics.

One of my study is to address the link between ASE and intratumoral
heterogenity.
I tried to get ASE pattern by implementing mamba but the overall process of
your approach is not clear to me.
I installed or downloaded related tools or scripts including mamba, GATK3.4
and Lappalainen's scripts (downloaded from her lab homepage).
Can you explain more detailed for how I could analyze ASE?

My previous attempts to follow the instruction of 'mamba' has been just at
the first stage.

1. ASEReadCounter (from GATK 3.4): .vcf --> allele_count.txt

I'm not sure the next step with the allele_count.txt data.
It would be wonderful if you help me understand clearer.

Thank you very much.

Sincerely,
Kyu-Tae Kim