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