PT  - JOURNAL ARTICLE
AU  - Sourya Bhattacharyya
AU  - Vivek Chandra
AU  - Pandurangan Vijayanand
AU  - Ferhat Ay
TI  - FitHiChIP: Identification of significant chromatin contacts from HiChIP data
AID  - 10.1101/412833
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 412833
4099  - http://biorxiv.org/content/early/2018/09/10/412833.short
4100  - http://biorxiv.org/content/early/2018/09/10/412833.full
AB  - Here we describe FitHiChIP (github.com/ay-lab/FitHiChIP), a computational method for identifying chromatin contacts among regulatory regions such as en-hancers and promoters from HiChIP/PLAC-seq data. FitHiChIP jointly models the non-uniform coverage and genomic distance scaling of HiChIP data, captures previously validated enhancer interactions for several genes including MYC and TP53, and recovers contacts genome-wide that are supported by ChIA-PET, pro-moter capture Hi-C and Hi-C data. FitHiChIP also provides a framework for differential contact analysis as showcased in a comparison of HiChIP data we have generated for two distinct immune cell types.