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vpc-ccg / sedef

Identification of segmental duplications in the genome
MIT License
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Different output from published results #24

Closed mchaisso closed 2 years ago

mchaisso commented 3 years ago

Hi, I'm trying to use sedef on mm8. There are a few missing dups: -- downloaded from csail: 352991 mm8.bed -- running sedef.sh with -j 16 as the only option 338320 out/mm8_final/final.bed

Some differences are expected over revisions, but there are some really large segdups that are missing.

The largest events with the corresponding line numbers are:

150493 178 150493 177 134550 846 134550 845 134492 3337 126247 3092 124653 1266 124653 1265 123007 2594 118273 2222

inumanag commented 2 years ago

Hi @mchaisso,

SEDEF is now deprecated. However, the reason for this behaviour (on top of my head, has been a long time since I implemented this) is probably due to the more stringent filtration of low-confidence SDs in later revisions.