bedpeintersect

A script for multi-intersect and annotation of HiC bedpee files

The script intersect the genome contacts represented in a bedpe file to all the bedfiles stored in a folder. Also annotate the closest gen each genomic region.

Requirements

python

• pandas
• pybedtools

External tools

• bedtools

Conda environment.

The conda or mamba environment to run this script can be created as follows.

conda create -n bedpeintersect-env -c bioconda -c conda-forge pybedtools pandas

or

mamba create -n bedpeintersect-env -c bioconda -c conda-forge pybedtools pandas

Files preparation.

Annotation files.

Currently this repo only ships processed annotation files for human genome GRCh38. This files path are hardcoded

The Ensemble annotation .gtf file was processed as follows:

1. Add the 'chr' string to the chromosome names.
2. Separate the 'gene' features in one file and the 'exon' and 'utr' features in other file.
3. Sort both files with bedtools (bedtools sort).

Bedpe input file.

The bedpe input file must contain only the 6 fields correspondint to a genomic contact/interaction, i.e.:

• anchor 1 chromosome name
• anchor 1 start position
• anchor 1 end position
• anchor 2 chromosome name
• anchor 2 start position
• anchor 2 end position

Bed files folder.

All the bedfiles to intersect must be in one folder.

Outputs.

The script generates 3 files:

1. "'melt_'": This is the melted version of the original bedpe. Thisi is, each anchor of each contact is in a separate line. Also an identifier name for each contact is created.
2. "'annotated_'": This is the oríginal bedbe with the name of each contact added and the results for each bed file.
3. "'table_'": Detailed results in table format, each line is an anchor. Contains the closest genomic feature for each genomic region.