How to Merge Regions in Multiple BED Files

In bioinformatics, you often need to merge the overlapping or book-ended genomic intervals into contiguous regions from the two or more BED files for genomic data analysis.

You can use various tools such as bedtools and bedops to merge two or more BED files.

Method 1: Using bedtools

If you have few BED Files:

cat file1.bed file2.bed | bedtools sort | bedtools merge > merged.bed

If you have many BED Files:

cat *.bed | bedtools sort | bedtools merge > merged.bed

Method 2: Using bedops

bedops --merge file1.bed file2.bed file3.bed > merged.bed

The following practical examples demonstrate how to use bedtools and bedops to merge multiple BED files.

Example 1: Using bedtools

bedtools can be used for overlapping or book-ended genomic intervals from the multiple BED files.

For example, you have the following three bed files (file1.bed, file2.bed, and file3.bed)

cat file1.bed
chr1    10      100
chr1    400     500

cat file2.bed
chr1    50      200
chr1    600     700

cat file3.bed
chr1    100     200
chr1    150     300
chr1    500     600

Now, merge the overlapping or book-ended genomic intervals from these three BED file

cat file1.bed file2.bed file3.bed | bedtools sort | bedtools merge > merged.bed

cat merged.bed
chr1    10      300
chr1    400     700

In above example, we used cat command to pipe the output to bedtools merge to merge the overlapping genomic intervals.

The merged output is saved in the merged.bed file.

Example 2: Using bedops

bedops can be used for merging overlapping genomic intervals into contiguous regions from the multiple BED files.

For example, you have the following three bed files (file1.bed, file2.bed, and file3.bed)

cat file1.bed
chr1    10      100
chr1    400     500

cat file2.bed
chr1    50      200
chr1    600     700

cat file3.bed
chr1    100     200
chr1    150     300
chr1    500     600

Now, merge the overlapping intervals into contiguous region from these three BED file

bedops --merge file1.bed file2.bed file3.bed > merged.bed

cat merged.bed
chr1    10      300
chr1    400     700

In above example, we used bedops --merge command to merge the overlapping genomic intervals from three BED files into contiguous regions.

The merged output is saved in the merged.bed file.