Error in loading forged BSgenome
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@jiazhou0116-24087
Last seen 10 months ago

Hi everyone,

I had forged BSgenome for cane toad reference genome. But I met error when running checkCuts function in msgbsR package. Just wondering whether you have any suggestions for this error.

> BSgenome.Rhinella.marina.UNSW.RM170330
cane toad genome:
# organism: Rhinella marina (cane toad)
# provider: UNSW
# provider version: RM170330
# release date: Mar. 2018
# release name: Rhinella marina (marine toad)
# 31391 sequences:
#   ONZH01000001.1 ONZH01000002.1 ONZH01000003.1 ONZH01000004.1 ONZH01000005.1 ONZH01000006.1
#   ONZH01000007.1 ONZH01000008.1 ONZH01000009.1 ONZH01000010.1 ONZH01000011.1 ONZH01000012.1
#   ONZH01000013.1 ONZH01000014.1 ONZH01000015.1 ONZH01000016.1 ONZH01000017.1 ONZH01000018.1
#   ONZH01000019.1 ONZH01000020.1 ONZH01000021.1 ONZH01000022.1 ONZH01000023.1 ONZH01000024.1
#   ONZH01000025.1 ONZH01000026.1 ONZH01000027.1 ONZH01000028.1 ONZH01000029.1 ONZH01000030.1
#   ...            ...            ...            ...            ...            ...           
#   ONZH01031363.1 ONZH01031364.1 ONZH01031365.1 ONZH01031366.1 ONZH01031367.1 ONZH01031368.1
#   ONZH01031369.1 ONZH01031370.1 ONZH01031371.1 ONZH01031372.1 ONZH01031373.1 ONZH01031374.1
#   ONZH01031375.1 ONZH01031376.1 ONZH01031377.1 ONZH01031378.1 ONZH01031379.1 ONZH01031380.1
#   ONZH01031381.1 ONZH01031382.1 ONZH01031383.1 ONZH01031384.1 ONZH01031385.1 ONZH01031386.1
#   ONZH01031387.1 ONZH01031388.1 ONZH01031389.1 ONZH01031390.1 ONZH01031391.1               
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator to access a given
# sequence)
> correctCuts <- checkCuts(cutSites = cutSites,
+                                      genome = "BSgenome.Rhinella.marina.UNSW.RM170330",
+                                      seq = "CCGG")

Error in loadFUN(x, seqname, ranges) : 
  trying to load regions beyond the boundaries of non-circular sequence "ONZH01000265.1"



md5-f322ac1373a484224f61a249aee063a1



> cutSites
GRanges object with 8589888 ranges and 0 metadata columns:
                                     seqnames    ranges strand
                                        <Rle> <IRanges>  <Rle>
  ONZH01000001.1:31660-31660:+ ONZH01000001.1     31660      +
  ONZH01000001.1:48877-48877:+ ONZH01000001.1     48877      +
  ONZH01000001.1:31873-31873:- ONZH01000001.1     31873      -
  ONZH01000001.1:49175-49175:- ONZH01000001.1     49175      -
    ONZH01000002.1:9415-9415:+ ONZH01000002.1      9415      +
                           ...            ...       ...    ...
  ONZH01031378.1:15692-15692:- ONZH01031378.1     15692      -
  ONZH01031385.1:10264-10264:+ ONZH01031385.1     10264      +
  ONZH01031389.1:47242-47242:+ ONZH01031389.1     47242      +
  ONZH01031389.1:47245-47245:+ ONZH01031389.1     47245      +
    ONZH01000955.1:7114-7114:- ONZH01000955.1      7114      -
  -------
  seqinfo: 31204 sequences from an unspecified genome; no seqlengths

Thanks,

Jia

BSgenome msgbsR • 169 views
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