SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control.

ABSTRACT: ChIP with reference exogenous genome (ChIP-Rx) is widely used to study histone modification changes across different biological conditions. A key step in the bioinformatics analysis of this data is calculating the normalization factors, which vary from the standard ChIP-seq pipelines. Choosing and applying the appropriate normalization method is crucial for interpreting the biological results. However, a comprehensive pipeline for complete ChIP-Rx data analysis is lacking. To address these challenges, we introduce SpikeFlow, an integrated Snakemake workflow that combines features from various existing tools to streamline ChIP-Rx data processing and enhance usability. SpikeFlow automates spike-in data scaling and provides multiple normalization options. It also performs peak calling and dif

SUBMITTER: Bressan D 

PROVIDER: S-EPMC11358820 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature