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Recommend parameters of borders detect

Open yizhang-zoey opened this issue 1 year ago • 1 comments

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.

yizhang-zoey avatar Jun 16 '23 10:06 yizhang-zoey