Maybe a basic question. I have RNA-Seq data from a tissue taken at different time points. The reads are in the SRA database (For example, here: SRR6314256).
For a gene with many different alternatively splice variants I want to get the relative read ratios between them. Say, I want to know if the splice variant A is more expressed than the splice variant B or C.
How do I do this?
I have tried using magic-blast using an artificial transcriptome database, containing only the gene of interest, with all the splice variants; to count the number of reads in each splice variant. But, I don't know how to infer the contribution of each variant, specially when most exons are common to at least 2 variants.