Hi, I have 2 bed files.
File 1: ref.bed
chr9 9383800 9493700 REGION
File 2: map.bed
chr9 9387448 9387482 PTPRD_EXON
I want to calculate a length of bases in an area overlapping between ref.bed and map.bed
So I used BEDOPS bedmap function as follows, and got the following result file.
$ bedmap --echo --bases ref.bed map.bed > result.bed
$ cat result.bed
chr9 9383800 9493700 REGION|34
Thus, this result file indicates that the length of bases in an overlapping area is "34bp".
However, I think the length might be incorrect.
Because, in this case, the overlapping area is chr9:9387448..9387482.
So, the length of overlapping area is 9387482-9387448+1 = "35bp".
Could you tell me whether my opinion is right?
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Apprentice
BED files are zero-based. This means that the number of bases in a BED element is simply the difference of the stop and start coordinates. See: What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordinate Systems
Thank you for your answer.
I could learn very important point about BED file.
BEDOPS is very useful tool. I want to continue utilizing that.
•
written
by
Apprentice
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