CUT&TAG and CUT&RUN are new molecular biology techniques that can find the locality of histone marks and transcription factor in DNA. Unlike the well-established ChIP-Seq protocol, CUT&TAG generates data with very little background signal, enriched peaks, and requires 10-fold less sequencing reads per sample. Due to the increased sparsity of signal in CUT&TAG, contemporary peak calling software like MACS2 and SEACR can have trouble identifying regions of histone / transcription factor enrichment in the genome; this problem is compounded by using lower-than-ideal quality sequencing libraries.
This repository compares the performance of gopeaks with MACS2 and SEACR in CUT&TAG / CUT&RUN data. The code for this analysis was adapted from the original CUT&TAG pipeline, with additional steps for MACS2 and SEACR peak calling. The additional steps will also include taking high-confidence peaks across biological replicates, plot the quality of peaks for each method, and evaluate the completeness of a method's peak call against a gold standard using ROC curves. A complete write-up of the methods can be found in the official paper here.
Once all the public data has been downloaded with src/custom/data_download.sh and the pipeline is finished, all the results will be found in data/figures. More results to come once the paper goes up!
Thank you to those who have contributed their time and effort to push the boundaries of progress.
CUT&TAG
Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10, 1930 (2019). https://doi.org/10.1038/s41467-019-09982-5
CUT&RUN
eLife 2017;6:e21856 doi: 10.7554/eLife.21856
SEACR
Meers, M.P., Tenenbaum, D. & Henikoff, S. Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Epigenetics & Chromatin 12, 42 (2019). https://doi.org/10.1186/s13072-019-0287-4
MACS2
Zhang, Y., Liu, T., Meyer, C.A. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9, R137 (2008). https://doi.org/10.1186/gb-2008-9-9-r137