How to find if our enhancer gene pair fall within TAD

Question

[rohitsatyam102]

Hello Everyone!!

I have a file containing genomic coordinates of enhancers and their associated gene coordinate. I am tasked to check if the coordinates fall within TAD boundaries. For that purpose, I have decided to use Dixon et al TAD matrix. However, I haven't ever done Hi-C analysis so I am confused about how to achieve my objective.

The TAD matrix contains the same coordinates in both the columns

##   chr1:770137-1250137     chr1  770137-1250137      *
##   chr1:1250137-1850140     chr1 1250137-1850140      *
##   chr1:1850140-2330140     chr1 1850140-2330140      *
##   chr1:2330140-3650140     chr1 2330140-3650140      *
##   chr1:4660140-6077413     chr1 4660140-6077413      *
##   chr1:6077413-6277413     chr1 6077413-6277413      *

How to interpret this? Any kind of help with be appreciated.

Answer 1

[ancient_learner]

Use Bedtools IntersectBed to see whether the positions of your enhancers overlap with TAD regions.

[rohitsatyam102]

Hi, I plan to use the Bedtools, however, I don't understand why the same coordinates are repeated twice in the file. Any idea?

[GouthamAtla]

I dont see any coordinates repeated from your example.

[rohitsatyam102]

I have a file that contains columns with same coordinate as shown below

Col1 .............................Col2

chr1:770137-1250137 chr1:770137-1250137

Why they are repeated twice? What does it mean? Also, I don't understand why the coordinates in the columns are continuous i.e. the end of each coordinate is the start of the next coordinate.

chr1:770137-1250137 chr1:1250137-1850140, chr1:1850140-2330140

[rohitsatyam102]

Okay so I found some explanation on the UCSC genome browser here:

But what does Start position of lower region and End position of upper region means

[GouthamAtla]

If you understand what are TADs, you will understand why most of them are continuously represented. If there exactly same coords repeated, you can remove duplicates.