A recent publication investigated splice variants of a gene I am interested in (using SMRT seq) and they described different/additional exons compared to what I find in NCBI or ENSEMBL.
I wanted to analyze splice variants and exon counts of this gene using the described exons from this publication in my RNA-seq data. I have a file with exon number and sequence.
How do I align my RNA-seq data to this list of exons? I thought about taking the normal .gtf file from ENSMBL and edit it to accommodate the exon changes. Is that the recommended way of doing so? And if so, how do I do it?
Thank you for your help!