LTR转座子的重新注释

Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants

library(LTRpred)
# de novo LTR transposon prediction of 'O. sativa'
LTRpred(
      genome.file = "Osativa.fa",
      cluster     = TRUE,
      cores       = 4,
      copy.number.est = FALSE,
      minlenltr   = 100,
      maxlenltr   = 5000,
      mindistltr  = 4000,
      maxdistltr  = 30000,
      mintsd      = 3,
      maxtsd      = 20,
      vic         = 80,
      overlaps    = "no",
      xdrop        = 7,
      motifmis    = 1,
      pbsradius   = 60,
      pbsalilen   = c(8,40),
      pbsoffset   = c(0,10),
      quality.filter = TRUE,
      n.orfs      = 0
      )
# import LTRpred output
Osativa_LTRpred <- read.ltrpred("Osativa_ltrpred/Osativa_LTRpred_DataSheet.tsv")