# bed_intersect: R Equivalent to Bedtools Intersect

`bedtools intersect`

is a useful tool in bioinformatics for finding the overlaps between genomic intervals from the BED file.

`bedtools intersect`

is a part of bedtools utilities which are developed to run as a command-line on a UNIX environment and could not be run on R software.

However, you can use `bed_intersect`

function from the R valr package for performing `bedtools intersect`

analysis in R.

The basic syntax for `bed_intersect`

function is:

```
# install.packages("valr")
# load package
library("valr")
bed_intersect(file1.bed, file2.bed)
```

Where, `file1.bed`

and `file2.bed`

contains the genomic intervals in BED format.

The following example explains how to find the overlapping intervals in R using `bed_intersect`

function (similar to `bedtools intersect`

).

Create two example genomic intervals to find the overlap,

```
# first BED file
bed1 <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 100, 500,
"chr1", 600, 700
)
# second BED file
bed2 <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 300, 500,
"chr1", 800, 900
)
```

We have created two genomic intervals in BED format using the tibble. Additionally, you can also import the data from the BED files.

Now, we will perform the `bedtools intersect`

analysis using `bed_intersect`

function to find the overlapping intervals between `bed1`

and `bed2`

genomic intervals.

```
# install.packages("valr")
# load package
library("valr")
bed_intersect(bed1, bed2)
# output
# A tibble: 1 × 6
chrom start.x end.x start.y end.y .overlap
<chr> <dbl> <dbl> <dbl> <dbl> <int>
1 chr1 100 500 300 500 200
```

You can see that there is one overlapping interval between the two intervals. There is a 200 bp overlap between the two intervals.

In addition, you can also visualize the overlap between the two genomic intervals using the `bed_glyph`

function.

```
# load package
library("valr")
bed_glyph(bed_intersect(bed1, bed2))
```

The additional parameters can also be used with `bed_intersect`

as described here.