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FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

ABSTRACT: Experimental methods for discovering RNA Binding Protein (RBP) binding sites on target RNAs have recently emerged which employ fusions of RBPs to RNA-editing enzymes (such asAPOBEC1 or ADAR) to “label” mRNA. However, off-target editing, genetic variants and sequencing errors can lead to false positives when using data derived from such approaches, and highlight a need for a robust, statistical approach to prioritizing confident binding sites.

ORGANISM(S): Homo sapiens

PROVIDER: GSE215252 | GEO | 2023/10/18

REPOSITORIES: GEO

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peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

Project description:High-resolution methods such as 4C and Capture-C enable the study of chromatin loops such as those formed between promoters and enhancers or CTCF/cohesin binding sites. An important aspect of 4C/CapC analyses is the identification of robust peaks in the data for the identification of chromatin loops. Here we present an R package for the analysis of 4C/CapC data. We generated 4C data for 10 viewpoints in 2 tissues in triplicate to test our methods. We developed a non-parametric peak caller based on rank-products. Sampling analysis shows that not read depth but template quality is the most important determinant of success in 4C experiments. By performing peak calling on single experiments we show that the peak calling results are similar to the replicate experiments, but that false positive rates are significantly reduced by performing replicates.

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