Fig. 1

RepEnTools is an automated repeat enrichment analysis package for ChIP-seq data. A In chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments chromatin is isolated and fragmented, by sonication or MNase treatment. The nucleosomes still carry the DNA sequence information. Affinity reagents such as antibodies or chromatin interacting protein domains are then used to retain specific targets while the rest of the chromatin is washed away. The enriched DNA fragments are then isolated and sequenced, typically using the Illumina platform. As a control, an equal amount of the input chromatin is also sequenced. The FASTQ files generated contain these DNA sequences. B RepEnTools is an automated repeat enrichment analysis package for ChIP-seq data. It takes as input the FASTQ files from two replicates of ChIP-seq and the respective input chromatin datasets, trims adapters, runs QC, and aligns the sequences to chm13v2, the first complete human genome assembly. The optimised settings result in rapid and low-cost alignments, while efficiency and quality are comparable to other popular software. The repeat masker (RMSK) annotation is then used to identify and count reads on individual instances of repeat elements (REs) genome-wide, summing them up for each type of RE. The data for all experimental replicates are then collected, normalised, compared to input for enrichment or depletion, analysed for reproducibility, and reported in tables. At the end, a volcano plot of significance log₁₀(p) versus fold-change log₂(ChIP/input) and bar diagrams of enrichment (ChIP/input) for the RE families visualise the enrichments and the depletions of RE types