ORF finding in DECIPHER
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tkirkland • 0
@78b8b275
Last seen 7 weeks ago
United States

I am trying to find ORFs in a file of fasta sequences. I get the error " Iter Models Start Motif Fold Init UpsNt Term RBS Auto Stop Genes 1 1Error in lenScr[w] <- (lenScr[w[1L] - 1] - lenScr[w[1L] - 2]) * seq_along(w) + : replacement has length zero"

Code should be placed in three backticks as shown below


> S_wt_orfs <- FindGenes(S_wt_fa, showPlot=TRUE, allScores=TRUE)

Iter  Models Start Motif  Fold  Init UpsNt  Term   RBS  Auto  Stop Genes
1          1Error in lenScr[w] <- (lenScr[w[1L] - 1] - lenScr[w[1L] - 2]) * seq_along(w) +  : 
  replacement has length zero"
ORF DECIPHER ORFhunteR • 106 views
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Entering edit mode

Thanks for reporting this issue.

  1. Which version of DECIPHER are you using? 2.18 has known bugs but 2.20 should be fine.
  2. Are your sequences a genome? DECIPHER is intended to find genes in (intronless) genomes.
  3. Please send me your sequences so that I can reproduce the error.
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