Open yeqiaoz opened 2 years ago
sa501428
commented
2 years ago @yeqiaoz can you show what the observed and control maps look in the all view without VS mode? It's not clear from this one picture that there is any error. i.e. the issue could be in the underlying file and not in Juicebox.
yeqiaoz
commented
2 years ago Hi Muhammad,
Here's an example on chromosome 8 of hg19. The first snapshot shows the two libraries individually, and the second one shows how they look if I use each other as control. The library on the left was aligned using Juicbox with ENZYME=none and the one on the right was aligned with HiC-Pro using MboI cutting sites and then converted to .hic. Any suggestions? Thank you!
sa501428
commented
2 years ago Can you normalize both maps? notice that there are two dropdowns, one for the main and one for the control.
yeqiaoz
commented
2 years ago I have a hypothesis about why this happened. One of the files was aligned with Juicer and the other was aligned with HiC-Pro and converted to .hic file. Both were aligned to the same reference hg19 genome with chromosomes named as "chr1, chr2, chrM, etc". Would you confirm whether Juicer pipeline saves the chromosomes as 1, 2, 3,... M in the .hic file, while the converters from other pipelines may have kept the chromosomes with "chr" and thus cause this problem? Thanks a lot!
sa501428
commented
2 years ago Can you share a picture with both of the maps normalized?
If the bug was as you described, I don't think it would have allowed the maps to load at all.
yeqiaoz
commented
2 years ago 
sa501428
commented
2 years ago How does it behave on Juicebox Web? (aidenlab.org/juicebox) Do things work correctly there?
When two .hic files are opened and viewed as "observed vs control" they completely shift out of place. See the attachment for an example. One is Micro-C aligned with ENZYME=none and the other one is HiC. Is there any setting that needs to be adjusted to avoid this?