DROPA

DROPA annotates DRIP-seq peaks to genes using gene expression information to assign strand-specific R-loop peaks within gene bodies and improve annotation accuracy for R-loop mapping.

Key Features:

• Customization: Allows selection of reference datasets and definition of gene features for annotation.
• Strand-Specific Annotation: Assigns R-loop peaks to the DNA template strand within gene bodies with a false positive rate of less than 7%.
• Performance and Accuracy: Identifies fewer false positive annotations compared to three widely used annotation tools.
• Integration into Pipelines: Produces outputs formatted for downstream analysis pipelines.
• Informative Outputs: Generates summary plots and performs statistical enrichment tests.

Scientific Applications:

• DRIP-seq R-loop mapping: Annotates co-transcriptional DRIP-seq peaks in the context of R-loop mapping.
• Histone mark IP-seq: Applicable to Histone mark IP-seq datasets.
• DNAse-seq: Applicable to DNAse-seq datasets.
• FAIRE-seq: Applicable to FAIRE-seq datasets.

Methodology:

DROPA utilizes gene expression information to assign DRIP-seq peaks to genes and to the DNA template strand within gene bodies, achieving a reported false positive rate below 7%.