Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development
First run R_Pipeline/00_Runall.R
Next run Published_Analysis.Rmd which will source the output of the pipeline.
All motif analysis was done using custom-built scripts for running MEME suite
tools from within R. These can be found in the Scripts/Nystlib/R/MEME_Utils.R
script. This functionality is currently being ported to an R package
DremeR.
I used meme 4.12.0 for DREME analysis, and AMEv5.1.0 for motif scanning. I have
saved the R data results from the AME and DREME runs in Data/ which are by
default loaded in the analysis notebook. To repeat the meme-suite runs
yourself, you'll have to manually remove the eval=F flags in the
corresponding notebook chunks. Note that using "shuffled" input for dreme runs
in this version breaks when setting a random seed, such that repeat iterations
using the same random seed will produce different results. This does not affect
overall conclusions of the manuscript. See notebook for details.
Raw data will be available at GSE141738 soon. This repo will also provide further description of the raw & processed data files for increased clarity.
Session info for my analysis can be found here.