Some old scripts from 2013 - 2014 that were usee for the parsing of histone ChIP-seq data. They were part of several exploratory analyses for projects carried out in the laboratory of T. Sauka-Spengler at the Weatherall Institute of Molecular Medicine at the University of Oxford, in the UK, working on datasets produced in chicken and zebrafish FACS-sorted neural crest cells.
In the following manuscript, authors investigated cis-regulatory elements in human neural crest cells and identified a pattern of primed enhancers surrounded by H3K27Ac peaks that co-localise with H3K4me1 peaks surrounding p300 and specific transcription factor binding. Here are some scripts useful to identify such patterns in FACs-sorted cells from chicken and zebrafish histone ChIP-seq.
Wyscocka lab paper that describes this phenomenon:
Rada-Iglesias, Alvaro, Ruchi Bajpai, Sara Prescott, Samantha A. Brugmann, Tomek Swigut, and Joanna Wysocka. "Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest." Cell stem cell 11, no. 5 (2012): 633-648.
Attempts at a peak called using wig files ... (old scripts)
Explanation coming soon ...