anti-mergeBED

[RockChalkJayhawk]

Does anyone know of a tool that works like mergeBed from BEDtools, bu instead reports the overlapping regions (and name) rather than the consolidated query?

Ex:
GeneA =======     =        ===========    =====
BeneB           =============

Final             =        ==

[kmcarr]

intersectBed

[RockChalkJayhawk]

intersectBed

IntersectBed will only work to tell me the intersection between two bed files. I want to find out the unique and non-unique portions of a single BED file.

[quinlana]

IntersectBed will only work to tell me the intersection between two bed files. I want to find out the unique and non-unique portions of a single BED file.

Could you please provide a more concrete example of what you want? For instance, maybe a toy file with your expected result and how it differs from what you get with intersect or merge? I think it's doable, but just want to be precise about what you want.

Best,
Aaron

[RockChalkJayhawk]

I have attached a better image to show what I am trying to do. Basically, when mergeBED occurs, I want to separate out exonic regions from overlapping genes that intersect and only where they intersect. mergeBED can use strand information so these two genes don't get merged, which is great. However, I also need to find the overlapping locations of intersecting genes - much like intersectBED does for two BED files - but since these are annotated in the same BED file, niether one will work.

In the example, I want to separate the last exon from Gene A into two parts - subsets of the exon that are unique to GeneA from the regions in geneA that intersect with exonic boundaries of Gene B.