search

vaquerizaslab / fanc

FAN-C: Framework for the ANalysis of C-like data
GNU General Public License v3.0
107 stars 14 forks source link

Negative value of coordinate in loop calling results #125

Open Qi-Yang-Bioinfo opened 2 years ago

Qi-Yang-Bioinfo commented 2 years ago

1 2

As you can see, there are weird negative values in loop calling results. X2 is the second column that represents the start point of the 1st loop anchor.

I used 10kb matrix to call chromatin loops. The code for loop calling is (same for chr2): fanc loops -c chr4 -t 92 --rh-filter -j -s -b ./chr4.bedpe ./chr4.hic ./chr4.loop

kaukrise commented 2 years ago

Hi, this is likely due to the loop centroid calculation. Did you plot the loops at those coordinates to see if there is an increase in signal?

Qi-Yang-Bioinfo commented 2 years ago

chr2 Yes, there is an increased signal at this locus. How can I deal with such negative values?

kaukrise commented 2 years ago

If all negative values correspond to actual loops / enriched regions, I think it would be valid to set them to 0. This would simply shift the left anchor the the chromosome start, which would then match the visible ("half") loop.