I am trying to use bedtools to compare a BED file with a GFF file.
The BED file is like below. Chr1 3641 5640 . . +
The GFF file is as follows. Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1 Chr1 TAIR10 protein 3760 5630 . + . ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1 Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1
I used the command
intersectBed –a A.bed –b B.gff –wa -wb to find overlaps.
However, my problem is: how to define intergenic, intron and intron-exon-overlapping or intergenic-gene-overlapping regions?
Thank you for any of your suggestions!