I am having a vcf file :
> seqlevels(D784G)
[1] "chrI" "chrII" "chrIII" "chrIV" "chrIX" "chrM" "chrV" "chrVI" "chrVII" "chrVIII"
[11] "chrX" "chrXI" "chrXII" "chrXIII" "chrXIV" "chrXV" "chrXVI"
> seqlevels(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
[1] "chrI" "chrII" "chrIII" "chrIV" "chrV" "chrVI" "chrVII" "chrVIII" "chrIX" "chrX"
[11] "chrXI" "chrXII" "chrXIII" "chrXIV" "chrXV" "chrXVI" "chrM"
> loc <- locateVariants(D784G, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, AllVariants())
Error in mergeNamedAtomicVectors(genome(x), genome(y), what = c("sequence", :
sequences chrI, chrII, chrIII, chrIV, chrIX, chrM, chrV, chrVI, chrVII, chrVIII, chrX, chrXI, chrXII, chrXIII, chrXIV, chrXV, chrXVI have incompatible genomes:
- in 'x': TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
- in 'y': sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3,
How to handle it?
Do I need to re arrange the seqlevels of my vcf file? If yes, then how?
Sincerely,
Deepak
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dktarathym •
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dktarathym •
Have you tried changing the genome with genome(D784G) <- "sacCer3"? That might solve the problem.
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Devon Ryan
Hi Devon,
Thank you so much.
It seems to work. Also, there are some warnings:
> genome(D784G) <- "sacCer3"
> loc <- locateVariants(D784G, txdb, AllVariants())
Warning messages:
1: In `start<-`(`*tmp*`, value = c(-1665L, -1462L, 480L, 8091L, 10046L, :
trimmed start values to be positive
2: In `end<-`(`*tmp*`, value = c(534L, 737L, 2679L, 10290L, 12245L, :
trimmed end values to be <= seqlengths
3: In `start<-`(`*tmp*`, value = c(-981575L, -802723L, -802656L, -802572L, :
trimmed start values to be positive
4: In `end<-`(`*tmp*`, value = c(1018425L, 1197277L, 1197344L, 1197428L, :
trimmed end values to be <= seqlengths
> loc
GRanges with 9269 ranges and 7 metadata columns:
seqnames ranges strand | LOCATION QUERYID TXID
<Rle> <IRanges> <Rle> | <factor> <integer> <integer>
chrI:18425_T/C chrI [ 18425, 18425] * | intergenic 1 <NA>
chrI [ 25479, 25479] - | coding 2 66
chrI [141030, 141030] + | coding 3 38
chrI [141030, 141030] + | promoter 3 39
chrI [141030, 141030] - | coding 3 103
... ... ... ... ... ... ... ...
chrXVI [869062, 869062] - | promoter 4301 6644
chrXVI [869062, 869062] - | coding 4301 6645
chrXVI [890346, 890346] + | coding 4302 6395
chrXVI [890346, 890346] + | promoter 4302 6396
chrXVI [890346, 890346] - | promoter 4302 6650
CDSID GENEID PRECEDEID
<integer> <character> <CharacterList>
chrI:18425_T/C <NA> <NA> YAL001C,YAL002W,YAL003W,...
68 YAL063C
39 YAL004W
<NA> YAL003W
105 YAL005C
... ... ... ...
<NA> YPR162C
6972 YPR163C
6709 YPR175W
<NA> YPR178W
<NA> YPR174C
FOLLOWID
<CharacterList>
chrI:18425_T/C YAL064C-A,YAL064W-B,YAL065C,...
... ...
---
seqlengths:
chrI chrII chrIII chrIV chrIX ... chrXII chrXIII chrXIV chrXV chrXVI
230218 813184 316620 1531933 439888 ... 1078177 924431 784333 1091291 948066
Are the seqlengths of D784G and txdb the same? I've never actually seen warnings about negative coordinates. Presuming you don't actually have any I don't know off-hand what's causing that.
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Devon Ryan
The seqlengths were same.
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dktarathym •
No clue then. I'd have to go through the source code or try it myself. Perhaps post this on the bioconductor board.
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Devon Ryan
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