Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
Pipeline for current version of cCREs on the hg38 and mm10 genomes. Please cite:
The ENCODE Project Consortium, Moore JE*, Purcaro MJ,* Pratt HE*, Epstein CB*, Shoresh N*, Adrian J*, Kawli T*, Davis CA*, Dobin A*, Kaul R*, Halow J*, Nostrand EL*, Freese P*, Gorkin DU*, Shen Y*, He Y*, Mackiewicz M*, Pauli-Behn F*, Williams BA, Keller CA, Zhang X, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM†, Myers RM†, Ren B†, Graveley BR†, Gerstein MB†, Pennacchio LA†, Snyder MP†, Bernstein BE†, Wold B†, Hardison RC†, Gingeras TR†, Stamatoyannopoulos JA†, Weng Z†
Nature, July 2020
First version of the pipeline which generated candidate Regulatory Elements (refered to as cREs) on the hg19 and mm10 genomes. This pipeline is no longer in use or maintained.