DoubleChEC program to identify transcription factor binding sites from mapped ChEC-seq data

ChIP-seq (chromatin immunoprecipitation followed by sequencing) is commonly used to identify genome-wide protein-DNA interactions. However, ChIP-seq often gives a low yield, which is not ideal for quantitative outcomes. An alternative method to ChIP-seq is ChEC-seq (Chromatin endogenous cleavage with high-throughput sequencing). In this method, the endogenous TF (transcription factor) of interest is fused with MNase (micrococcal nuclease) that non-specifically cleaves DNA near binding sites. Compared to the original ChEC-seq method, the modified version requires far less amplification. Since MACS3 failed to identify peaks in data generated from the modified ChEC-seq method, a new peak finder has been developed specifically for it.
There are three functions in the peak_finder/. callpeaks() is used to identify peaks from BAM files. goanalysis() is used to make GO (Gene Ontology) term plots from peaks. bedtomeme() is a wrapper function to perform MEME analysis in R after MEME Suite is inst..., ****EXCERPTED FROM BIORXIV PREPRINT; SEE PREPRINT OR PUBLISHED PAPER FOR REFERENCES AND DETAILS****
Yeast strains
All yeast strains were derived from BY4741.  A C-terminal micrococcal nuclease fusion was introduced to the protein of interest through transformation and homologous recombination of PCR-amplified DNA. Primers were designed with 50-bp of homology to the 3’ end of the coding sequence of interest.  The 3xFLAG-MNase with a KanR marker was amplified from pGZ108 (Zentner et al., 2015) and transformed into BY4741 as previously described.  Successful transformation was confirmed by immunoblotting and PCR, followed by sequencing.
Lyophilized DNA oligonucleotides were resuspended in molecular-grade water to a concentration of 100 µM.  For ligation, the following pair of oligonucleotides were annealed to produce the Y-adapter: Tn5ME-A (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’) and Y-Adapt-i5 R (5’-CTGTCTCTTATACACATCTTCATAGTAATCATC-3’).  For Tn5 Tagmentation, the following i7 oligonucle..., , # DoubleChEC TF binding site finder

## Introduction

ChIP-seq (chromatin immunoprecipitation followed by sequencing) is commonly used to identify genome-wide protein-DNA interactions. However, ChIP-seq often gives a low yield, which is not ideal for quantitative outcomes. An alternative method to ChIP-seq is ChEC-seq (Chromatin endogenous cleavage with high-throughput sequencing). In this method, an endogenous TF (transcription factor) fused to MNase (micrococcal nuclease) cleaves DNA near binding sites. This package is designed to identify high-confidence binding sites from cleavage patterns from ChEC-seq2, a variant form of ChEC-seq.

There are three functions in the *`peak_finder/`*. `callpeaks()` is used to identify peaks from single-end mapped reads input as BAM files. `goanalysis()` is used to make GO (Gene Ontology) term plots from peaks. `bedtomeme()` is a wrapper function to perform [MEME analysis](https://meme-suite.org/meme/tools/meme) in R **after [MEME Suite](https://meme-...