RepeatMasker reader

Script to read RepeatMasker data for downstream analysis. Data is downloaded from https://www.repeatmasker.org/species/hg.html and the following file is used: hg38.fa.out.gz

Considering the size of the data, this should be downloaded to a high-performance computing cluster (ideally >16GB) memory in order to open and read the file.

Dependencies

• R version 3.6.1 (or above)
• R libraries lincluding rtracklayer and GenomicRanges
• BASH
• Linux-powered high-performance computing cluster with a SLURM workload manager

Usage

The script should be run in the following manner

sbatch repeat.masker.running.sh

Output

The output of the script is two files:

• A reformatted text file called "repeatmasker.reformat.txt" which will contain RepeatMasker data
• An RData file containing a GRange object indicating repeat elements in the genome by chromosome location, repeat name, repeat class, and repeat family