Hey All,

I am using GRCh38.p7 reference genome using GENCODE realease 25 (ensemble 85 annotation(GTF)). I have a set of cordinates (transcripts) and i want to know how many and which exons lie in between the cordinates and then get the sequence (using the given annotation and assembly).

Geting the sequence is not a problem but finding the exons in between the cordinates, i need help with this.

  chromosome    end         start   Strand
    chr4        48104901    48114402    --
    chr13       20067390    20051433    ++
    chr14       55619312    55612019    ++
    chr14       65075774    65078036    --
    chr14       49825867    49831361    --
    chr1       28476291     28473554    ++

Thanks.