MARGI is a protocol for mapping RNA-DNA contacts on a genome-wide scale, analogous to Hi-C methods which map DNA-DNA contacts. In situ MARGI (iMARGI) is the successor of the MARGI technique, requiring fewer input cells and less time than required by MARGI.
The 4DN iMARGI data processing pipeline is adapted from the Zhong iMARGI pipeline. Its primary components are cleaning and alignment of reads, parsing of alignments into pairs, and merging and aggregation of pairs. To learn more about the original pipeline or experimental protocol, please reference the iMARGI Pipeline documentation.
The primary modifications are:
- An additional output pairs file from the parsing step
- The addition of 4DN standard resolutions and modification of flag usage in the creation of cool files
- Swapping of column order for DNA and RNA in
cooler cload pairs, and
- Additional test files and CWLs for running the pipeline.
The iMARGI Docker, used in all steps of the pipeline, can be found at https://hub.docker.com/r/4dndcic/imargi/v1.1.1_dcic_4