I aligned the RNAseq reads to the diploid (hybrid genome) and calculated the TPM (transcripts per million) values for my samples using EMASE. So, the TPM values are reported for each gene_id and haplotype. I want to do ASE variation analyses within the samples. My thought is that applying DE approaches to it would be fine, but the analyses should focus for the difference with in the samples and also check if the ASE differences for any given gene is/are consistent across samples.
I have came across edgeR, DeSeq, DeSeq2, kalliso sleuth. But, I am wondering if someone could suggest which of these tools would be best to work with my data.
Note: I posted the same question on google groups just to expedite the analyses. If this violates the policy of question posting please let me know.
Thanks, - Bishwa K.