diff --git a/docs/benchmark.md b/docs/benchmark.md index e738248de124d1d5a5f52861edcfdfab17e6427e..4f366a11cc6b12b87114cf72de276e13034577f9 100644 --- a/docs/benchmark.md +++ b/docs/benchmark.md @@ -56,18 +56,23 @@ Normal vs iterative | Normal vs parasplit | Normal vs cutsite :-------------------------:|:-------------------------:|:-------------------------:  |  |  +The balanced matrices do not add any information, there is no differences observed when the matrices are balanced. + #### Parasplit vs cutsite All chromosomes (4kb, norm to 1) | Chromosome 3 (1kb, norm to 1) | Chromosome 3 (1kb, not normalized) :-------------------------:|:------------------------:|:------------------------:  |  |  + 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. -#### 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 @@ -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. +#### Distance law (4kb, on normal alignment) + + +The filter option deletes the loops and weird reads + ## Conclusion balblaba diff --git a/docs/images/counts_filters_4kb.png b/docs/images/counts_filters_4kb.png new file mode 100644 index 0000000000000000000000000000000000000000..fb75aa1f17c5e6c3fb12e2c4444b24d40c00a309 Binary files /dev/null and b/docs/images/counts_filters_4kb.png differ