So I'm trying to find out if certain regions of interest interact from these published results. I am no specialist when it comes to Hi-C data, or bioinformatics clearly, but I do have a strong theoretical background and have watched and read tutorials on how to process RAW reads. So, when I finally felt confident to process the reads, I went to the accension and picked up these files which were described in the paper as RAW reads but they obviously are not. I've tried plugging this file into SeqMonk but it would'nt take it because this file is weird?
I want to know what these columns are because I've asked the authors but to no solid reply. Also, how do I modify this file for better visualization?
Self described as:
Library strategy: Hi-C Hi-C reads were aligned using Bowtie 0.12.7 with default parameters and “-m 1” PCR duplicate reads were removed GC content, mappability, and fragment length effects were normalized as described in Hou et al., Molecular Cell 48, 471-484 (2012). Genome_build: dm3 Supplementary_files_format_and_content: Hi-C processed files are in a modified bed format. Each row lists the chromosome and the start and end coordinates of two interacting bins as well as the normalized interaction frequency between these two bins
There are no headers on this file and to me this is not a traditional .hic file. What do you interpret these columns to be?! Also apparently in column "I" 0 = + strand, 16 = - strand...