Is it possible to run an Allele Specific Expression (ASE) experiment with just RNA-Seq data?

Question

[utsafar]

Is it possible to run an Allele Specific Expression (ASE) experiment with just RNA-Seq data? For example there is no genome data for crocus sativus (Saffron) but there are some RNA-Seq data.

Answer 1

[GouthamAtla]

You may need to assemble the transcriptome, then map the reads back to the transcriptome, call SNPs and look for SNPs that show allelic imbalance. If you do not have data from different biological samples ( i.e different genotypes ), it would be difficult the believe the results from ASE.

[GiV17]

I don't understad. What is the correct pipeline for Allele Specific Expression? Thanks