I have installed bedtool and tried fastafromBED but it looks like when I ask for positions 1 to 25, it gives me 2 to 25 instead in the output. How come?
I had posted that as a comment and got a first reply:
"BED format uses zero-based, half-open coordinates, so the first 25 bases of a sequence are in the range 0-25 (those bases being numbered 0 to 24). – Keith James♦ Mar 12 at 16:33"
So BED coordinates are different from GFF3 for example? How to confidently reformat columns of start-stop intervals before extracting coordinates using BEDtools?
Thanks in advance!