Developer: Annnkatrin Bressin (bressin@molgen.mpg.de) Date: 3.2.2023

Code was developed for UNIX systems and must be executed via the command line. Software requirements are listed below. All paths to the listed applicatipons must be part of the $PATH variable. For more information see https://wiki.archlinux.org/title/Bash#Configuration_files.

Software and Versions:

standard unix command line utilities such as paste, cut, join, awk, ln, mkdir , dirname, ...

Rscript (R) version 4.2.2 (2022-10-31) (default) * required R libraries will be installed automatically Rscript-4.0.5 (R) version 4.0.5 * required for DiffBind

Python 3.10.8 * required libraries: - pyBigWig 0.3.18 (https://github.com/dpryan79/pyBigWig) - numpy 1.23.4 (1.23.4)

gunzip (gzip) 1.12

bedGraphToBigWig v 4

bigWigToBedGraph

bedtools v2.30.0

deeptools 3.2.1 * computeMatrix, plotHeatmap, computeMatrixOperations,...

samtools 1.16.1

STAR 2.7.3a * please call executable file STAR_2.7.3a

FastQC v0.11.9

cutadapt 4.1

starcode-v1.1

chromHMM 1.19 (http://compbio.mit.edu/ChromHMM/)