CIPHER

CIPHER provides integrative workflows for processing and analyzing next-generation sequencing (NGS) datasets to identify regulatory elements and transcriptional programs.

Key Features:

• Comprehensive Dataset Support: Supports ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq datasets.
• Integration of Open Source Tools: Combines open-source software packages, in-house scripts, and Docker containers to process single-ended and paired-end datasets.
• Systematic Workflow Pipelines: Implements raw sequence evaluation; read trimming and adapter removal; read mapping and quality filtering; visualization track generation; and extensive quality control assessment.
• Downstream Analysis Capabilities: Provides ChIP-seq narrow and broad peak calling, peak annotation, motif identification; RNA-seq differential gene expression analysis; MNase-seq nucleosome positioning; DNase-seq mapping of DNase hypersensitive sites, site annotation, and motif identification; GRO-seq nascent transcription analysis; and ATAC-seq chromatin accessibility characterization.
• Enhanced "Analysis" Mode: Enables enhancer discovery and integrative analyses across multiple datasets to extract combined biological insights.

Scientific Applications:

• Regulatory network and transcriptional program identification: Integration of multiple NGS assays to identify regulatory networks that drive transcriptional programs.
• Genomic regulatory element mapping: Discovery and annotation of enhancers, promoters, and other regulatory elements using ChIP-seq, DNase-seq, ATAC-seq, and motif analysis.
• Chromatin accessibility and nucleosome positioning: Characterization of chromatin accessibility and nucleosome organization using ATAC-seq, DNase-seq, and MNase-seq.
• Differential and nascent transcription analysis: Differential gene expression analysis from RNA-seq and nascent transcription profiling from GRO-seq.
• Standardized, reproducible NGS workflows: Application of consistent pipelines to improve reproducibility of multi-assay genomic analyses.

Methodology:

Integrates open-source tools, in-house scripts, and Docker containers to process single-ended and paired-end NGS data through raw sequence evaluation, adapter trimming/read trimming, read mapping and quality filtering, visualization track generation, and quality control; performs ChIP-seq peak calling (narrow and broad), peak annotation, motif identification, RNA-seq differential expression, MNase-seq nucleosome positioning, DNase-seq DHS mapping and site annotation, GRO-seq nascent transcription analysis, ATAC-seq accessibility characterization, and dataset integration for enhancer discovery.