Hello Biostars community!
I would like to get the coordinates of all the intergenic regions of a single chromsome. can you please give me your suggestions how to do this?
Right now, I have a genes.bed file and the sizes of all the chromosomes of my model organism. I think I need to make a bed file for the chromosomes and intersect the two.
Do I start with 1 (as start position) and end with chromosome size (as end position) ? can I make individual bed files per chromosome where each bed file has a single row where all start positions for all chromosomes is 1? I already tried this and it doesn't work, I get no output from bedtools :(
I appreciate very much your suggestions.