Hi-C workflow

[adthrasher]

Continuation of #25

[adthrasher]

This proposal is for the deposition of raw Hi-C sequencing data in St. Jude Cloud. Jinghui Zhang instructed the creation of a mechanism for distributing raw data, particularly that belonging to her paper with Tom Look (https://pubmed.ncbi.nlm.nih.gov/29284669/). Subsequent conversations with other stakeholders suggest that raw data is of little utility or interest to the field. The field has adopted .hic files, which were a feature of Juicer, but now can be generated by additional tools. These files include the interacting pairs and are a starting point for analysis.

This proposal assumes that BAM files, which are essentially intermediate files in Hi-C analysis, are available for conversion to unaligned BAMs. Alternative options include distributing the FASTQ file directly or merging and converting to unaligned BAMs. We could also adopt an approach to perform a more complete harmonization workflow which would enable us to distribute analysis files (.hic).

[adthrasher]

Updated the RFC with the general flow of the Hi-C workflow that is based on HiC-Pro.