Question: Allele specific analysis
2
gravatar for halo22
4.1 years ago by
halo22180
Indianapolis, IN
halo22180 wrote:

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?

rna-seq alignment next-gen • 1.1k views
ADD COMMENTlink modified 4.0 years ago by Ron1000 • written 4.1 years ago by halo22180

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

ADD REPLYlink written 4.1 years ago by geek_y11k

Mostly do a network analysis of risk alleles.

ADD REPLYlink written 4.1 years ago by halo22180
1
gravatar for sbombin
4.0 years ago by
sbombin10
sbombin10 wrote:

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

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

ADD COMMENTlink written 4.0 years ago by sbombin10
1
gravatar for colindaven
4.0 years ago by
colindaven2.3k
Hannover Medical School
colindaven2.3k wrote:

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.

ADD COMMENTlink written 4.0 years ago by colindaven2.3k
0
gravatar for Ron
4.0 years ago by
Ron1000
United States
Ron1000 wrote:

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

ADD COMMENTlink written 4.0 years ago by Ron1000

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

ADD REPLYlink written 4.0 years ago by geek_y11k

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.

ADD REPLYlink written 4.0 years ago by Ron1000
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