Recommend parameters of borders detect

[yizhang-zoey]

Hi
I'm a green hand of Hi-C.
What are the recommended parameters of chromosight detect --pattern borders?
Especially min-dist and min-dist.
What I have used is

chromosight detect \
--threads 8 \
--min-dist 10000 \
--min-dist 1000000 \
--pattern $pattern \
$PAIRS_FILE \
$output_prefix

But the contact map plotted by .tsv file is strange.
Thanks.

[axelcournac]

Hi,
For borders patterns, they are found at the inner diagonal so by default the parameters are the following:
"max_dist": 0,
"min_dist": 0,
If you want to explore the whole map, you can change them, it depends on the organism you are working on: for large genomes like human it is important to set a reasonable limit so that the computation time for the convolution product is not too long (although it is possible to scan the whole human genome in a few hours).
Here are a few examples for loop detections that you can find on the page: https://github.com/koszullab/chromosight_analyses_scripts

Best