When used to perform the Arima-HiC assay, the Arima-HiC+ kit is compatible with a broad range of sample types, including:
For analysis of Arima HiChIP data, we recommend the Arima-MAPS 2.0 tool. The latest update is available here (https://github.com/ijuric/MAPS), and the original MAPS pipeline is available here (https://github.com/ijuric/MAPS/releases/tag/v1.1.0). Benchmarking with MAPS, FitHiChIP, HICCUPS, and CriSPRi-validated genomics loops revealed that MAPS has the highest sensitivity with a moderate false-positive rate while minimizing computational time. The MAPS 2.0 pipeline has been updated to include the MACS2 ChIP-seq peak calling algorithm, which allows ChIP-seq peak calling from Arima-HiChIP data as well as improved usability by the expansion of command line options.
A test dataset to verify the Arima-MAPS installation and configuration is available at ftp://ftp-arimagenomics.sdsc.edu/pub/MAPS/test_data/.