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Question: makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
1
gravatar for RJ
8 days ago by
RJ10
RJ10 wrote:

Hi,

It seems 'makeTxDbFromUCSC' currently cannot load refGene in hg19. Could you help me to fix this? Here's what I did:

> txdb <- makeTxDbFromUCSC(genome="hg19", tablename="refGene")
Error in .tablename2track(tablename, session) : 
  UCSC table "refGene" is not supported

 

I have confirmed the existence of this track:

browseUCSCtrack("hg19", "refGene")

 

I have updated everything:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] rtracklayer_1.38.3     GenomicFeatures_1.30.3 AnnotationDbi_1.40.0   Biobase_2.38.0         GenomicRanges_1.30.3  
 [6] GenomeInfoDb_1.14.0    IRanges_2.12.0         S4Vectors_0.16.0       AnnotationHub_2.10.1   BiocGenerics_0.24.0   
[11] BiocInstaller_1.28.0  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16                  compiler_3.4.2                XVector_0.18.0               
 [4] prettyunits_1.0.2             progress_1.1.2                bitops_1.0-6                 
 [7] tools_3.4.2                   zlibbioc_1.24.0               biomaRt_2.34.2               
[10] digest_0.6.15                 bit_1.1-12                    lattice_0.20-35              
[13] RSQLite_2.1.0                 memoise_1.1.0                 Matrix_1.2-14                
[16] DelayedArray_0.4.1            shiny_1.0.5                   DBI_0.8                      
[19] yaml_2.1.18                   GenomeInfoDbData_1.0.0        stringr_1.3.0                
[22] httr_1.3.1                    Biostrings_2.46.0             grid_3.4.2                   
[25] bit64_0.9-7                   R6_2.2.2                      BiocParallel_1.12.0          
[28] XML_3.98-1.10                 RMySQL_0.10.14                magrittr_1.5                 
[31] blob_1.1.1                    matrixStats_0.53.1            GenomicAlignments_1.14.2     
[34] Rsamtools_1.30.0              htmltools_0.3.6               SummarizedExperiment_1.8.1   
[37] assertthat_0.2.0              mime_0.5                      interactiveDisplayBase_1.16.0
[40] xtable_1.8-2                  httpuv_1.3.6.2                stringi_1.1.7                
[43] RCurl_1.95-4.10              
 

 

ADD COMMENTlink modified 6 days ago by James W. MacDonald46k • written 8 days ago by RJ10
3
gravatar for James W. MacDonald
6 days ago by
United States
James W. MacDonald46k wrote:

Unless you are answering your own question, please don't use the 'Add your answer' box. the ADD COMMENT link is what you should use to add comments.

The issue here is that the UCSC Genome Browser is a bit of a moving target, and they do tend to make changes that end up breaking our tools. In this case they have retroactively changed the hg19 track names to correspond to those for hg38, so now we have to make changes to accommodate their changes.

I have made the necessary changes to the devel version of GenomicFeatures, and it should propagate through the build system within the next couple of days. This is an inauspicious time to make changes, as the release version of Bioconductor is now locked and I cannot make the changes for the release version. Once the new release is out in a couple of weeks it won't be an issue, but for now we are in that time where the release can't be updated, so if you want the changes you will have to install the development version of R and then the development version of Bioconductor to get the updated/fixed version of GenomicFeatures.

Anyway, before the fix we have this from supportedUCSCtables:

> supportedUCSCtables()
             tablename          track           subtrack
1            knownGene     UCSC Genes               <NA>
2        knownGeneOld8 Old UCSC Genes               <NA>
3        knownGeneOld7 Old UCSC Genes               <NA>
4        knownGeneOld6 Old UCSC Genes               <NA>
5        knownGeneOld4 Old UCSC Genes               <NA>
6        knownGeneOld3 Old UCSC Genes               <NA>
7             ccdsGene           CCDS               <NA>
8          xenoRefGene   Other RefSeq               <NA>
9             vegaGene     Vega Genes Vega Protein Genes
10      vegaPseudoGene     Vega Genes   Vega Pseudogenes
11             ensGene  Ensembl Genes               <NA>
12             acembly  AceView Genes               <NA>
13             sibGene      SIB Genes               <NA>
14       nscanPasaGene         N-SCAN    N-SCAN PASA-EST
15           nscanGene         N-SCAN             N-SCAN
16             sgpGene      SGP Genes               <NA>
17              geneid   Geneid Genes               <NA>
18             genscan  Genscan Genes               <NA>
19            exoniphy       Exoniphy               <NA>
20          ncbiRefSeq    NCBI RefSeq         RefSeq All
21   ncbiRefSeqCurated    NCBI RefSeq     RefSeq Curated
22 ncbiRefSeqPredicted    NCBI RefSeq   RefSeq Predicted
23     ncbiRefSeqOther    NCBI RefSeq       RefSeq Other
24       ncbiRefSeqPsl    NCBI RefSeq  RefSeq Alignments

And you can see that the refGene table isn't there. After the fix we have

 supportedUCSCtables()
             tablename          track           subtrack
1        knownGeneOld8 Old UCSC Genes               <NA>
2        knownGeneOld7 Old UCSC Genes               <NA>
3        knownGeneOld6 Old UCSC Genes               <NA>
4        knownGeneOld4 Old UCSC Genes               <NA>
5        knownGeneOld3 Old UCSC Genes               <NA>
6             ccdsGene           CCDS               <NA>
7              refGene    NCBI RefSeq        UCSC RefSeq
<snip>

And

> makeTxDbFromUCSC("hg19","refGene")
Download the refGene table ... OK
Download the hgFixed.refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: hg19
# Organism: Homo sapiens
# Taxonomy ID: 9606
# UCSC Table: refGene
# UCSC Track: NCBI RefSeq
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Entrez Gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 70013
# exon_nrow: 270643
# cds_nrow: 219560
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2018-04-13 12:20:12 -0700 (Fri, 13 Apr 2018)
# GenomicFeatures version at creation time: 1.31.10
# RSQLite version at creation time: 2.1.0
# DBSCHEMAVERSION: 1.2

 

 

ADD COMMENTlink written 6 days ago by James W. MacDonald46k

This is Great! Thanks a lot for your help! 

ADD REPLYlink written 6 days ago by RJ10
0
gravatar for C
7 days ago by
C0
Norway
C0 wrote:

I had same error with customProDB and it turns out that USCS stops provide 'refGene' table mentioned by author's Email reply. Not sure about the solution yet :( 

ADD COMMENTlink written 7 days ago by C0
0
gravatar for RJ
6 days ago by
RJ10
RJ10 wrote:

This is a bit strange, because I have confirmed the refGene is still in UCSC by using:

browseUCSCtrack("hg19", "refGene")

 

Any other alternative ways I can get the annotation/GTF/GFF3 of refGene in hg19?

 

 

ADD COMMENTlink written 6 days ago by RJ10
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