Cranial Neural Crest Ectodermal Mesenchymal Differentiation
This analysis pipeline was created for the PhD thesis of Dr. Maria Replogl in the lab of Dr. Ava Udvadia at the University of Wisconsin -- Milwaukee.
Authors: Jason W. Bacon, Dr. Paul W. L. Auer (Sleuth analysis script)
The analysis compares gene expression data from RNA-Seq and chromatin accessibility data from ATAC-Seq at three time points in differentiating Mus Musculus neural and chondrocyte cells in culture. It includes standard differential expression and differential accessibility analyses as well as custom scripts and newly developed C code (peak-classifier) to aid in correlating gene expression and chromatin accessibility.
Much of this analysis is modeled on the work of Dr. Andrea Rau:
https://github.com/andreamrau/OpticRegen_2019
It was originally developed in fall 2019 and spring 2020, but has since been overhauled to simplify the scripts, make them more readable, and make them easily adaptable to other data sets. Adapting the scripts for a reanalysis of the Optic Regen data with the latest tools has proven to be quite simple.
This pipeline was developed and run on a FreeBSD cluster, with some testing also performed on a CentOS 7 cluster, both running the SLURM batch system. It is designed to be highly portable and easily adaptable to new data sets.
The entire pipeline can be completed in a day or two using ~64 cores.
All sbatch scripts artificially set default SLURM environment variables so that they can be tested on a single sample outside the SLURM environment.
Programs used in the scripts are assumed to be in the user's PATH. If not, add appropriate steps to the sbatch scripts. ( Altering PATH, activating environments or containers, etc. in .bashrc or other startup scripts is not recommended, as attempting to support various programs within a single environment is complicated and prone to cause problems. )
The install-programs scripts will install all necessary software on a FreeBSD cluster or workstation.
See the following links for FreeBSD setup:
http://acadix.biz/desktop-installer.php http://acadix.biz/spcm.php