MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Fig 1
MAPS workflow contains three major components: pre-processing, normalization and long-range interaction determination. Valid read pairs are obtained after pre-processing and then grouped to short-range reads or long-range reads depending on the genomic distance between two ends (1Kb is used). The long-range reads are further classified into the “AND”, “XOR” or “NOT” set. MAPS only considers the “AND” and “XOR” set of bin pairs for normalization and identification of the statistically significant long-range chromatin interactions. Short-range reads are used to estimate and correct for biases introduced by the ChIP procedure.