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!
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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