Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.

ABSTRACT: Chromatin accessibility assays have revolutionized the field of transcription regulation by providing single-nucleotide resolution measurements of regulatory features such as promoters and transcription factor binding sites. ATAC-seq directly measures how well the Tn5 transposase accesses chromatinized DNA. Tn5 has a complex sequence bias that is not effectively scaled with traditional bias-correction methods. We model this complex bias using a rule ensemble machine learning approach that integrates information from many input k-mers proximal to the ATAC sequence reads. We effectively characterize and correct single-nucleotide sequence biases and regional sequence biases of the Tn5 enzyme. Correction of enzymatic sequence bias is an important step in interpreting chromatin accessibility as

SUBMITTER: Wolpe JB 

PROVIDER: S-EPMC10236359 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature