How to make an Exon Junction BED file from ENSEMBL

Question

[QVINTVS_FABIVS_MAXIMVS]

I want to make an exon junction bed file to use for olego for the CAST strain of mouse. Ensembl has the reference genome and GTF files for this strain. Are there any tools to make an exon junction bed file for this strain?

Answer 1

[Alex Reynolds]

A: How can I count read that falls into exon-intron and exon-exon junction?

[QVINTVS_FABIVS_MAXIMVS]

Thanks I think this will do it friendo