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Fig. 3 | BMC Bioinformatics

Fig. 3

From: RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data

Fig. 3

Overview of RGT-viz and motif analysis. a RGT-viz provides several tests for regions versus regions and visualization tools for regions versus signals by taking BED and BAM files as input. b Motif matching detects binding sites for a set of TFs against multiple genomic regions. The motifs were collected from public repositories such as UniPROBE, JASPAR, and HOCOMOCO. The position weight matrix (PWM) for each TF is used to calculate a binding affinity score per position. The genomic regions are usually obtained by peak calling based on ChIP-seq or ATAC-seq data

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