Question: Bed Coordinates For Negative/Reverse Strand
1
gravatar for brianrepko
7.2 years ago by
brianrepko10
brianrepko10 wrote:

I understand from the BED "standard" at UCSC that it is a residue, 0-based, half-open system. And all the examples make sense - on the positive strand.

For example - http://alternateallele.blogspot.de/2012/03/genome-coordinate-conventions.html - is a great post about this.

However for the negative strand - which end is the half-open end? Is it always the largest value or is it the end "not-used"?

I found this link - http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms - to be a hot mess as the numbers are reversed - which is not what I want.

If I'm converting a negative strand gene annotation from GTF to BED - is it always GTF(start,end)--> BED(start-1,end) - even for negative strand?

bed • 4.2k views
ADD COMMENTlink modified 7.2 years ago by KCC4.0k • written 7.2 years ago by brianrepko10
3
gravatar for KCC
7.2 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

For BED, It's the same regardless of the strand. The first base in the interval is at the start value and the last is end-1. The first base in the genome is 0.

For GTF, it's the same regardless of strand, the first base in the interval is at the start value and the last is end. The first base in the genome is 1.

So, as you say GTF:start,end = BED:start-1,end

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by KCC4.0k
1
gravatar for Matt LaFave
7.2 years ago by
Matt LaFave290
San Diego, CA
Matt LaFave290 wrote:

I believe (start-1,end) would be the correct conversion for both strands, since the start and end position of the BED are just read left to right, regardless of the orientation of the feature.

ADD COMMENTlink written 7.2 years ago by Matt LaFave290
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