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Question: makeTxDbFromGFF Problem - GenomicFeatures R package
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Hi!

I am trying to make a TxDB using GenomicFeature R package using my gff3 file but I don't understand the error that the package thought out.

Does anyone know what is happening?

WHAT I AM DOING

library(GenomicFeatures)
gff_path <- '/path/to/gff3'

makeTxDbFromGFF(file = gff_path, format = 'gff3')

WHAT HAPPENS

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in .normarg_makeTxDb_transcripts(transcripts) : 
  values in 'transcripts$tx_strand' must be "+" or "-"
In addition: Warning messages:
1: In makeTxDbFromGRanges(gr, metadata = metadata) :
  The following transcripts were dropped because their exon ranks could not be inferred (either because the exons are
  not on the same chromosome/strand or because they are not separated by introns): MGAL10A032099T3, MGAL10A092172T1,
  MGAL10A092173T1, MGAL10A092174T1, MGAL10A092176T1, MGAL10A092182T1, MGAL10A092185T1, MGAL10A092186T1,
  MGAL10A092189T1, MGAL10A092190T1, MGAL10A092196T1, MGAL10A092203T1, MGAL10A092205T1, MGAL10A092208T1,
  MGAL10A092210T1, MGAL10A092212T1, MGAL10A092213T1, MGAL10A092214T1, MGAL10A092215T1, MGAL10A092216T1,
  MGAL10A092220T1, MGAL10A092223T1, MGAL10A092226T1, MGAL10A092227T1, MGAL10A092232T1, MGAL10A092234T1,
  MGAL10A092236T1, MGAL10A092239T1, MGAL10A092240T1, MGAL10A092244T1, MGAL10A092255T1, MGAL10A092258T1,
  MGAL10A092261T1, MGAL10A092263T1, MGAL10A092264T1, MGAL10A092265T1, MGAL10A092272T1, MGAL10A092275T1,
  MGAL10A092276T1, MGAL10A092280T1, MGAL10A092286T1, MGAL10A092288T1, MGAL10A092291T1, MGAL10A092293T1,
  MGAL10A092296T1, MGAL10A092302T1, MGA [... truncated]
2: In .reject_transcripts(bad_tx, because) :
  The following transcripts were rejected because they have CDSs that cannot be mapped to an exon: MGAL10A092225T1,
  MGAL10A092365T1, MGAL10A092368T1
3: In .find_exon_cds(exons, cds) :
  The following transcripts have exons that contain more than one CDS (only the first CDS was kept for each exon):
  MGAL10A092192T1, MGAL10A092230T1, MGAL10A092231T1, MGAL10A092350T1, MGAL10A092383T1

SESSION INFO

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2         GenomicRanges_1.28.6   GenomeInfoDb_1.12.3   
[6] IRanges_2.10.5         S4Vectors_0.14.7       BiocGenerics_0.22.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               compiler_3.4.1             plyr_1.8.4                 XVector_0.16.0            
 [5] bitops_1.0-6               tools_3.4.1                zlibbioc_1.22.0            biomaRt_2.32.1            
 [9] digest_0.6.12              bit_1.1-12                 lattice_0.20-35            RSQLite_2.0               
[13] memoise_1.1.0              tibble_1.3.4               gtable_0.2.0               rlang_0.1.4               
[17] Matrix_1.2-12              DelayedArray_0.2.7         DBI_0.7                    yaml_2.1.15               
[21] GenomeInfoDbData_0.99.0    rtracklayer_1.36.6         Biostrings_2.44.2          bit64_0.9-7               
[25] grid_3.4.1                 XML_3.98-1.9               BiocParallel_1.10.1        ggplot2_2.2.1             
[29] blob_1.1.0                 matrixStats_0.52.2         GenomicAlignments_1.12.2   scales_0.5.0              
[33] Rsamtools_1.28.0           SummarizedExperiment_1.6.5 colorspace_1.3-2           RCurl_1.95-4.8            
[37] lazyeval_0.2.1             munsell_0.4.3
ADD COMMENTlink 24 months ago manuelmendoza • 40
Entering edit mode
1

The strand column of your gff3 file must contain "+" or "-"

ADD REPLYlink 24 months ago
andrew.j.skelton73
5.7k

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