Entering edit mode
4.0 years ago
apoire27
•
0
I have a set of coordinates for a theoretical gene and I want to make a gene neighborhood for it with a gff file for the organism is this possible without using bedtools?
my coordinate sets look as follows
sample:start:stop:strand
NZOQ01000006.1_108 : 113072:14901:1
Can I ask why you are specifying that exception?
bedtools slop
generally will do this.I was under the impression you need the input coordinates to be in bed format to use bedtools and mine are just the coordinates in a text file I have output from a hmm run. is this incorrect?
You could convert those easily to BED format.
Based on the comment you have below you are looking for
bedtools intersect
orbedops
equivalent (@Alex may be by with that answer).What do you mean by a "gene neighbourhood"? Do you mean a fixed distance either side of the gene? Or do you want to use the midpoint between genes?
I am looking for the closest +/-10 genes from my coordinates