When we look in detail the difference between parasplit and cutsite, we observed that parasplit gives more contacts, which is obvious when we look at the no normalized matrices diff (right).
When we look in detail the difference between parasplit and cutsite, we observed that parasplit gives more contacts, which is obvious when we look at the no normalized matrices diff (right).
For the alignment, we seem to get more contact with parasplit.
For the alignment, we seem to get more contact with parasplit.
#### Distance law (4kb)
#### Distance law (4kb, without filters)


For the iterative alignment, even if there is less contacts than parasplit or cutsite in general, there may be more cis contacts.
## Comparison of filtering options
## Comparison of filtering options
...
@@ -111,5 +116,10 @@ No filter vs filter (cutsite) | No filter vs filter pcr (cutsite) |
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@@ -111,5 +116,10 @@ No filter vs filter (cutsite) | No filter vs filter pcr (cutsite) |
We still have the line on the diagonal for the filtering option, same as with normal alignment, regardless of the color which is depending of which condition is place as the first or second matrix in the formula, and intensity of color which is higher for parasplit and cutsite, due to their high number of contact.
We still have the line on the diagonal for the filtering option, same as with normal alignment, regardless of the color which is depending of which condition is place as the first or second matrix in the formula, and intensity of color which is higher for parasplit and cutsite, due to their high number of contact.
#### Distance law (4kb, on normal alignment)

The filter option deletes the loops and weird reads