Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
Pipeline for ENCODE4 cCREs (V4 - current version) on the hg38 and mm10 genomes. Please cite:
Jill E. Moore†, Henry E. Pratt, Kaili Fan, Nishigandha Phalke, Jonathan Fisher, Shaimae I. Elhajjajy, Gregory Andrews, Mingshi Gao, Nicole Shedd, Yu Fu, Matthew C Lacadie, Jair Meza, Mohit Ganna, Eva Choudhury, Ross Swofford, Nina P. Farrell, Anusri Pampari, Vivekanandan Ramalingam, Fairlie Reese, Beatrice Borsari, Michelle Yu, Eve Wattenberg, Marina Ruiz-Romero, Milad Razavi-Mohseni, Jinrui Xu, Timur Galeev, Michael A. Beer, Roderic Guigó, Mark Gerstein, Jesse Engreitz, Mats Ljungman, Timothy E. Reddy, Michael P. Snyder, Charles B Epstein, Elizabeth Gaskell, Bradley E Bernstein, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Ali Mortazavi, Anshul Kundaje, Zhiping Weng†
bioRxiv, December 2024, https://doi.org/10.1101/2024.12.26.629296
Code for generating V3 cCREs on the hg38 and mm10 genomes. Pipeline is identical to V2. 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
Pipeline for ENCODE3 cCREs (V2) 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.