allelic specific expression with Kallisto

Question

[Assa Yeroslaviz]

Hi all,

I was wondering if someone can tell me where I can find more about how to do an allele-specific Expression (ASE) analysis using either Kallisto or different tools. I have read the description in the Kallisto paper about ASE, but didn't really understood what I need to do to enable such analysis. Do I need to run the Kallisto analysis differently than the default parameters?

In general I would like to know, if there is a good workflow/tool/description on how to do an allele-specific expression analysis with RNA-Seq data.

any help would be appreciate.

thanks Assa

[grant.hovhannisyan]

Do you have a phased genome?

[Assa Yeroslaviz]

I don't know what that is.

[grant.hovhannisyan]

Phased genome is a genome where two alternative haplotypes are distinguished. For example, in case of human with phased genome you would have both sequences from each of homologous chromosomes. Have a look at this review - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0762-6 Also there is a recent software that might help you https://www.nature.com/articles/ncomms12817

In general this is a quite new topic, so don't expect any mature and well established approaches like in usual expression analysis :)

[h.mon]

See this presentation:

D. pseudoobscura genome = FlyBase reference

D. persimilis genome = Illumina reads mapped to Dpse reference using bwa Variants IDed using GATK HaploypeCaller Genome reconstructed using AlleleSeq vcf2diploid

And read RSEM tutorial:

[...] RSEM is also able to quantify allele-specific expression. To quantify allele-specific expression, we need to build RSEM references from phased sequences and provide RSEM a map from phased haplotypes to isoforms and then to genes using the --allele-to-gene-map option.

They won't give an straight answer but it will take you some steps closer.