Quantifying allele-specific expression imbalance using NGS

[jastop]

Hi all,
I am totally new to NGS. May I solicit your ideas and advice for the new pipeline to quantify allele-specific expression (ASE) imbalance in an F1 hybrid.

I have RNAseq libraries from, say, control and blast-infected. The questions I would like to ask are:
1) I was able to call SNPs using samtools, now what shall I do next to measure transcripts from each of the heterozygous SNPs, given F1 hybrid? (Or have I done the right thing, that is to call SNPs?)
2) what software do you recommend to measure allelic imbalance or ASE?

Thanks a lot,
jastop

[nika]

I would like to know that to...

Hi everyone,

I see there is no reply to this post, but there's more of us that would need the same advice.

I've recently read two interesting papers on the subject:
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data, Skelly et al, Genome Research, 2011

AlleleSeq: analysis of allele-specific expression and binding in a network framework, Rozowsky et al, Molecular Systems Biology, 2011

Aside from the "pipeline", they seem to have a different statistical approach to the question.
The Rozowssky paper offers a "pipeline" to download, but it doesn't seem to be user friendly.

On the other hand, there are some more ready to use pipelines, like GENE-Counter, but I haven't seen many papers published that have used it?

Any word of advice on the matter would be welcome...

Best,
nik

[arrchi]

agree

eager to know if there is any new development.