This pipeline is intended for work within the UCR computer cluster as it assumes access to several software packages. Some of the steps also require a large amount of memory to execute. It is strongly advised for the user to execute the scripts through submission to the cluster, rather than using a local node.
Each step is labeled and should be followed in sequential order from 1_QC to 8_functional_enrichment.
The folders for the steps contain a script for the corresponding function and links to manuals for the required software modules.
All scripts can be found in their respective folders to download or can be accessed in the directory:
/bigdata/messaoudilab/ssure003/Projects/Maob_Mom_CD14_ATAC/paper-jan2019/scripts/
Contributors: Suhas Sureshchandra, Brian Ligh