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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.


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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 ...


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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 ...


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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 ...


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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 ...


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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 -...


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