Question: How to find if our enhancer gene pair fall within TAD
0
gravatar for rohitsatyam102
4 months ago by
rohitsatyam102200 wrote:

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.

sequencing gene R genome • 143 views
ADD COMMENTlink modified 4 months ago by ancient_learner630 • written 4 months ago by rohitsatyam102200
0
gravatar for ancient_learner
4 months ago by
India
ancient_learner630 wrote:

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

ADD COMMENTlink written 4 months ago by ancient_learner630

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

ADD REPLYlink written 4 months ago by rohitsatyam102200

I dont see any coordinates repeated from your example.

ADD REPLYlink written 4 months ago by geek_y11k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by rohitsatyam102200

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

ADD REPLYlink modified 4 months ago • written 4 months ago by rohitsatyam102200

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.

ADD REPLYlink written 4 months ago by geek_y11k
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