A program for analyzing proximity ligation experiments from mapped files in the Fastq or SAM format to 1) generate a list of chimeric interactions with their coordinates, sequence, and folding energy, 2) plot contact density map of selected genes, 3) generate intra-/intermolecular RNA structure of any selected regions
The pipeline uses hybrid-min and optionally hybrid-min-ss, but there's no mention of it in the setup steps. Installation/compiling of Unafold should be added as a setup step before running this pipeline.
I should also raise a concern that Unafold seems to be very difficult to acquire. Luckily my system already had it installed, but for the benefit of other users who don't have it, I'd recommend considering alternative, more freely available software for this step if possible.
The pipeline uses hybrid-min and optionally hybrid-min-ss, but there's no mention of it in the setup steps. Installation/compiling of Unafold should be added as a setup step before running this pipeline.
I should also raise a concern that Unafold seems to be very difficult to acquire. Luckily my system already had it installed, but for the benefit of other users who don't have it, I'd recommend considering alternative, more freely available software for this step if possible.