Allele specific analysis

Question

[halo22]

Is anyone doing a allele specific expression analysis study? I would love to know all possible methods to analyze allele's. Also is there a way to do a allele network map?

[GouthamAtla]

What kind of analysis are you looking for ? Its a very broad topic.

[halo22]

Mostly do a network analysis of risk alleles.

Answer 1

[sbombin]

AlleleSeq could perform analysis of allele-specific expression and binding in a network

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208341/

Answer 2

[colindaven]

A difficult topic: this is a great paper on what to do and what not to do, since there have been many false starts in the field.

https://www.ncbi.nlm.nih.gov/pubmed/25730764

HAve a look at Supplement table S2 especiialy for how to control for challenges.

Answer 3

[Ron]

You can use pysam http://pysam.readthedocs.io/en/latest/usage.html you would need a VCF file along with this.

[GouthamAtla]

May I know how does this answer the original question ? Is it a comment to any of the above answers or comments ?

[Ron]

This answers the question - Pysam can be used to do Allele Specific Expression Analysis.Basically,it requires a sam/bam file and a vcf file for this purpose.