Allele Specific Expression Analysis

Question

[Susmita Mandal]

Hey All,

Does anyone have any experience in Allele specific gene expression analysis? Any recommended tools and pipelines? And any idea on how to retain only RNA-seq reads overlapping known SNP sites that differ between the two distinct parental genomes? I have fair knowledge of RNA Seq and SNP analysis. But ASE is nowhere explained properly. Anything would be helpful

EDIT: I have created two pseudo parental genomes and mapped my samples onto both of them using STAR and with options --outFilterMismatchNmax 0 ( Allowing for 0 mismatches ) and --outFilterMultimapNmax 1 (Allow no multi-mapped reads ). This ensures allele-specific mapping of most SNP-containing reads to only one strain-specific genome. I am interested only in the X chromosome ( X linked genes ). I don't know what to do after this.

Susmita

[Ankit]

Hi, After alignment you can use bedtools to intersect your bam or bed on SNP coordinates and extract only those reads which overlap SNPs.

[ta_awwad]

Hi Susmita, Have you by any chance managed to analyse your allele-specific RNA-seq data? best TA

[Susmita Mandal]

Yes I did managed to do the analysis and some more. But its not allele specific RNA-Seq data. I do allele specific on RNA-Seq data. Any questions?

[ta_awwad]

yes that is what i meant .. Do you mind sharing the workflow you have used with me?

Tamer

Answer 1

[Tm]

You can have a look at ASEReadCounter of GATK or SCALE.

[Susmita Mandal]

I do not have single cell RNA Seq data. But I'll look into the ASEReadCounter of GATK for sure!

[Tm]

You can also refer this article where they have used STAR for mapping purpose followed by ASEReadCounter tool for ASE analysis. Here they have used human lymphoblastoid cell line RNAseq data and not single cell RNAseq data.

[monaallouba]

does ASEReadCounter work for INDELs? as I tried using it and did not get any results

[Susmita Mandal]

Try HaplotypeCaller from GATK or VarScan2.

Answer 2

[grant.hovhannisyan]

Also take a look at PHASER software https://www.nature.com/articles/ncomms12817. The authors are famous in the field.