how to get intergene coordinates for a single chromosome?

Question

[Zee_S]

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.

Thank You!

[natasha.sernova]

Hopefully it may help:

Extract coordinates of adjacent genes for each provided intergenic regions from gff file

https://support.bioconductor.org/p/66003/

https://genome.ucsc.edu/goldenpath/help/multiRegionHelp.html

https://stackoverflow.com/questions/29253412/finding-intergenic-regions