Question: Allele specific analysis
2
gravatar for halo22
3.3 years ago by
halo22130
Indianapolis, IN
halo22130 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 • 986 views
ADD COMMENTlink modified 3.1 years ago by Ron980 • written 3.3 years ago by halo22130

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

ADD REPLYlink written 3.3 years ago by geek_y10.0k

Mostly do a network analysis of risk alleles.

ADD REPLYlink written 3.3 years ago by halo22130
1
gravatar for sbombin
3.2 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 3.2 years ago by sbombin10
1
gravatar for colindaven
3.1 years ago by
colindaven1.8k
Hannover Medical School
colindaven1.8k 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 3.1 years ago by colindaven1.8k
0
gravatar for Ron
3.1 years ago by
Ron980
United States
Ron980 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 3.1 years ago by Ron980

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 3.1 years ago by geek_y10.0k

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 3.1 years ago by Ron980
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