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4 votes
Accepted

What is the correct way to map Hi-C data with bwa mem?

See here, in particular slide #10 from the tutorial: bwa mem -5SPM ref.fa read1.fq read2.fq > out.sam Here, -SP disables ...
user172818's user avatar
  • 6,535
3 votes

BWA doesn't recognize HiC options

Your link with those command line options is 1 year old. Looks like that version of bwa is 6 years old. You probably should update.
swbarnes2's user avatar
  • 1,941
2 votes
Accepted

Get a single number representing the contact probability between a pair of genomic loci using HiC data

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 ...
James Hawley's user avatar
  • 1,384
1 vote

Loop and TAD calling from HiC reads using HOMER

Without being terribly familiar with your data or the tool or the tutorial, I think that there is a simple technical explanation: your statistical power to detect TADs will be much higher than your ...
Maximilian Press's user avatar
1 vote
Accepted

Installing HiC-Pro issues

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 ...
Jeff's user avatar
  • 177
1 vote
Accepted

How to identify the reference genome assembly used to create a .hic file?

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. ...
user345394's user avatar
1 vote
Accepted

Where to assign a read pair when a mate spans a HiC bin boundary?

[Old question, but possibly still relevant to answer.] This will not necessarily be rare. One or the other of the mates could span the ligation junction itself, in which case your read start and end ...
Maximilian Press's user avatar
1 vote

What is the correct way to map Hi-C data with bwa mem?

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. ...
burger's user avatar
  • 2,199

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