Hi!
I've spent some time debugging why sim3C seems to give too many read pairs where one read is at the end of a chromosome and the other at the beginning. Typically a visualization of a HiC-matrix looks like this, even on a completely random simulated genome:
Note the high interaction at the top right and lower left of the chromosome pictured.
After digging through the code, I noticed this:
I think it's problematic that this is not documented in any way or has not been fixed. I would put a warning in the Readme about this so users are aware.
Hi!
I've spent some time debugging why sim3C seems to give too many read pairs where one read is at the end of a chromosome and the other at the beginning. Typically a visualization of a HiC-matrix looks like this, even on a completely random simulated genome:
Note the high interaction at the top right and lower left of the chromosome pictured.
After digging through the code, I noticed this:
I think it's problematic that this is not documented in any way or has not been fixed. I would put a warning in the Readme about this so users are aware.