See here, in particular slide #10 from the tutorial:
bwa mem -5SPM ref.fa read1.fq read2.fq > out.sam
Here, -SP disables pairing. The Aiden lab and this paper also use a similar command line. Beware that there are many Hi-C pipelines, but not many are using bwa-mem.
If you're reading this, I can only assume that's because you had trouble installing HiC-Pro too. I was finally able to install from source and run the software, so here is how I did it, giving detail to the error that I was hit with and the clues I used to solve the puzzles and get through installing this program:
From Source To install from source, you ...
I could install HiC-Pro using conda when creating a separate environment (which I always do for side-projects), and then pull the conda build of HiC-Pro:
conda create --name HiCPro python=2.7
conda activate HiCPro
conda install -c davebx hicpro
Not sure what conda.sh is that you describe, sometimes tricky to get random code from GitHub running. Give it a go ...
The fundamental unit of a Hi-C contact is the nearest restriction enzyme cut site.
This is where each mate in a read pair from a Hi-C library comes from and is mapped to when converting sequencing data into a contact matrix.
Because the distance to the nearest cut site is variable at different genomic positions, and depth of coverage of any single locus is ...
Turns out HiC file does store such metadata.
straw tool from Aiden Lab contains a script (read_hic_header.py) that prints out the metadata from a given HiC file. Usage: read_hic_header.py <hic file or URL> [verbose]
In order to obtain the metadata in the form of a dictionary, one may consider using a function of the same tool that is currently ...
There are some interesting suggestions from the HiCExplorer developers:
Mates have to be mapped individually to avoid mapper specific
heuristics designed for standard paired-end libraries.
# map the reads, each mate individually using
# for example bwa
# bwa mem mapping options:
# -A INT score for a sequence match, which scales options -...