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Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling
Aslihan Karabacak,
Antje Hirsekorn,
Ricardo Wurmus,
Dilmurat Yusuf,
Uwe Ohler
Genome Biology
2019
20 1 42
DOI
PubMed
Abstract
We demonstrate that the impact of bias correction on footprinting performance is greater for DNase-seq than for ATAC-seq and that DNase-seq footprinting leads to better performance. It is possible to infer concordant footprints by using replicates, highlighting the importance of reproducibility assessment. The results presented here provide an overview of the advantages and limitations of footprinting analyses using ATAC-seq and DNase-seq.
Additional info
Software page and tool download
GitHub Repository
