How to prepare the segmental duplication file for non-human species?

calkan / sonic

Some Organism's Nucleotide Information Container

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How to prepare the segmental duplication file for non-human species? #11

Closed bampress closed 4 years ago

bampress commented 5 years ago

I'm doing research on plant species, and I don't have a finished segmental duplication file for it. How can I generate this input file for sonic? Any advice? Many thanks ^_^

calkan commented 5 years ago

try SEDEF: https://www.ncbi.nlm.nih.gov/pubmed/30423092 code: https://github.com/vpc-ccg/sedef

bampress commented 5 years ago

ok，I'll have a try. Many thanks for your timely reply!

milesandersonmn commented 2 years ago

I am in the same situation, but SEDEF is deprecated. The replacement BISER produces a BEDPE file. Will SONIC accept the BEDPE format?

calkan commented 2 years ago

Hi Miles

you can easily convert it to BED with something like

awk '{OFS="\t"; print $1,$2,$3"\n"$4,$5,$6}' biserdups.bedpe | bedtools merge > biserdups.bed