Slightly customized version of the ENCODE ATAC-seq v1 pipeline. Made to run on Penn's high performance cluster (PMACS). The ENCODE ATAC-Seq pipeline v1 specifications are listed in this google doc: (specs at https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit#heading=h.9ecc41kilcvq
https://docs.google.com/document/d/1mpQp8NtI195oHWYb8pb_frV969209UIRCni3_gaWihw/edit
This pipeline uses specific features of the PMACS high performance cluster at Penn. Some of the pipeline's reference files and required software are in a folder that is only available to Raj lab members. Please email me if you would like me a copy of these reference files.