I am doing RNA-seq analysis for allele-specific gene expression. To do that, two mouse strains were hybrid. I do have reference fasta files for both but do no not have gff file for one strain.
So far, I have done the mapping and alignment using STAR and I got Aligned.sortedByCoord.out.bam. Now I would like to compare read counts that are mapped same exons or genes to find allele-specific gene expression. But I am not sure which tool to use. I know both HTseq and featureCounts require gff file. Any ideas ??