HTseq or featureCounts without gff file

Question

[arta]

Hi,

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 ??

Answer 1

[Devon Ryan]

You should be using one of the many available ASE programs rather than trying to roll your own solution.

Anyway, this is what lapels and suspenders are for. You then only need an annotation for one parental line.

[arta]

Thanks Devon, I will look them.