ChIPQC GRCh38 usage yields "Unsupported annotation:hg38"
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Coby Viner ▴ 50
@coby-viner-10939
Last seen 3.6 years ago
University of Toronto, Canada

I am unable to use ChIPQC with GRCh38/hg38. When I attempt to, via experiment <- ChIPQC(samples, annotation="hg38"), I obtain:

Compiling annotation...
Error in getAnnotation(annotation, AllChr = chromosomes) : 
  Unsupported annotation:hg38
Calls: ChIPQC -> getAnnotation

 

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.3 (Final)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ChIPQC_1.8.5               DiffBind_2.0.2            
 [3] SummarizedExperiment_1.2.3 Biobase_2.32.0            
 [5] GenomicRanges_1.24.2       GenomeInfoDb_1.8.1        
 [7] IRanges_2.6.1              S4Vectors_0.10.1          
 [9] BiocGenerics_0.18.0        ggplot2_2.1.0             
[11] BiocInstaller_1.22.3      

loaded via a namespace (and not attached):
 [1] edgeR_3.14.0                             
 [2] splines_3.3.0                            
 [3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 
 [5] gtools_3.5.0                             
 [6] assertthat_0.1                           
 [7] latticeExtra_0.6-28                      
 [8] amap_0.8-14                              
 [9] RBGL_1.48.1                              
[10] Rsamtools_1.24.0                         
[11] Category_2.38.0                          
[12] RSQLite_1.0.0                            
[13] backports_1.0.2                          
[14] lattice_0.20-33                          
[15] limma_3.28.10                            
[16] digest_0.6.10                            
[17] RColorBrewer_1.1-2                       
[18] XVector_0.12.0                           
[19] checkmate_1.8.0                          
[20] colorspace_1.2-6                         
[21] Matrix_1.2-6                             
[22] plyr_1.8.4                               
[23] GSEABase_1.34.0                          
[24] chipseq_1.22.0                           
[25] XML_3.98-1.4                             
[26] pheatmap_1.0.8                           
[27] ShortRead_1.30.0                         
[28] biomaRt_2.28.0                           
[29] genefilter_1.54.2                        
[30] zlibbioc_1.18.0                          
[31] xtable_1.8-2                             
[32] GO.db_3.3.0                              
[33] scales_0.4.0                             
[34] brew_1.0-6                               
[35] gdata_2.17.0                             
[36] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
[37] BiocParallel_1.6.2                       
[38] annotate_1.50.0                          
[39] GenomicFeatures_1.24.2                   
[40] survival_2.39-4                          
[41] magrittr_1.5                             
[42] systemPipeR_1.6.2                        
[43] fail_1.3                                 
[44] gplots_3.0.1                             
[45] hwriter_1.3.2                            
[46] GOstats_2.38.0                           
[47] graph_1.50.0                             
[48] tools_3.3.0                              
[49] BBmisc_1.9                               
[50] stringr_1.1.0                            
[51] sendmailR_1.2-1                          
[52] munsell_0.4.3                            
[53] locfit_1.5-9.1                           
[54] AnnotationDbi_1.34.3                     
[55] Biostrings_2.40.2                        
[56] caTools_1.17.1                           
[57] grid_3.3.0                               
[58] RCurl_1.95-4.8                           
[59] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
[60] rjson_0.2.15                             
[61] AnnotationForge_1.14.2                   
[62] bitops_1.0-6                             
[63] base64enc_0.1-3                          
[64] gtable_0.2.0                             
[65] DBI_0.4-1                                
[66] reshape2_1.4.1                           
[67] R6_2.1.3                                 
[68] GenomicAlignments_1.8.3                  
[69] Nozzle.R1_1.1-1                          
[70] dplyr_0.4.3                              
[71] rtracklayer_1.32.1                       
[72] KernSmooth_2.23-15                       
[73] stringi_1.1.1                            
[74] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[75] BatchJobs_1.6                            
[76] Rcpp_0.12.7                              
[77] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[78] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2

 
chipqc ChIPQC • 2.3k views
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Dear Viner, Just load or install the package: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") library(TxDb.Hsapiens.UCSC.hg38.knownGene)

Best wishes, Siddik

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@thomas-carroll-7019
Last seen 2.0 years ago
United States/New York/The Rockefeller …
hi Coby, Yes, GRCh38 is not supported explicitly in the current release but I intend to add to next Bioconductor release. You can however add any annotation you wish to ChIPQC using the methods discussed in this thread. creating custom genome annotation for the ChIPQC package If you can't wait for upcoming release (I believe end of October) I can also provide the annotation off-list if you email directly and again you can provide this to ChIPQC as described in thread above. best, tom On Wed, Sep 14, 2016 at 7:14 PM, Coby Viner [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Coby Viner <https: support.bioconductor.org="" u="" 10939=""/> wrote Question: > ChIPQC GRCh38 usage yields "Unsupported annotation:hg38" > <https: support.bioconductor.org="" p="" 87096=""/>: > > I am unable to use ChIPQC with GRCh38/hg38. When I attempt to, via experiment > <- ChIPQC(samples, annotation="hg38"), I obtain: > > Compiling annotation... > Error in getAnnotation(annotation, AllChr = chromosomes) : > Unsupported annotation:hg38 > Calls: ChIPQC -> getAnnotation > > ------------------------------ > > > > > sessionInfo() > R version 3.3.0 (2016-05-03) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: CentOS release 6.3 (Final) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] ChIPQC_1.8.5 DiffBind_2.0.2 > [3] SummarizedExperiment_1.2.3 Biobase_2.32.0 > [5] GenomicRanges_1.24.2 GenomeInfoDb_1.8.1 > [7] IRanges_2.6.1 S4Vectors_0.10.1 > [9] BiocGenerics_0.18.0 ggplot2_2.1.0 > [11] BiocInstaller_1.22.3 > > loaded via a namespace (and not attached): > [1] edgeR_3.14.0 > [2] splines_3.3.0 > [3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 > [4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 > [5] gtools_3.5.0 > [6] assertthat_0.1 > [7] latticeExtra_0.6-28 > [8] amap_0.8-14 > [9] RBGL_1.48.1 > [10] Rsamtools_1.24.0 > [11] Category_2.38.0 > [12] RSQLite_1.0.0 > [13] backports_1.0.2 > [14] lattice_0.20-33 > [15] limma_3.28.10 > [16] digest_0.6.10 > [17] RColorBrewer_1.1-2 > [18] XVector_0.12.0 > [19] checkmate_1.8.0 > [20] colorspace_1.2-6 > [21] Matrix_1.2-6 > [22] plyr_1.8.4 > [23] GSEABase_1.34.0 > [24] chipseq_1.22.0 > [25] XML_3.98-1.4 > [26] pheatmap_1.0.8 > [27] ShortRead_1.30.0 > [28] biomaRt_2.28.0 > [29] genefilter_1.54.2 > [30] zlibbioc_1.18.0 > [31] xtable_1.8-2 > [32] GO.db_3.3.0 > [33] scales_0.4.0 > [34] brew_1.0-6 > [35] gdata_2.17.0 > [36] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 > [37] BiocParallel_1.6.2 > [38] annotate_1.50.0 > [39] GenomicFeatures_1.24.2 > [40] survival_2.39-4 > [41] magrittr_1.5 > [42] systemPipeR_1.6.2 > [43] fail_1.3 > [44] gplots_3.0.1 > [45] hwriter_1.3.2 > [46] GOstats_2.38.0 > [47] graph_1.50.0 > [48] tools_3.3.0 > [49] BBmisc_1.9 > [50] stringr_1.1.0 > [51] sendmailR_1.2-1 > [52] munsell_0.4.3 > [53] locfit_1.5-9.1 > [54] AnnotationDbi_1.34.3 > [55] Biostrings_2.40.2 > [56] caTools_1.17.1 > [57] grid_3.3.0 > [58] RCurl_1.95-4.8 > [59] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 > [60] rjson_0.2.15 > [61] AnnotationForge_1.14.2 > [62] bitops_1.0-6 > [63] base64enc_0.1-3 > [64] gtable_0.2.0 > [65] DBI_0.4-1 > [66] reshape2_1.4.1 > [67] R6_2.1.3 > [68] GenomicAlignments_1.8.3 > [69] Nozzle.R1_1.1-1 > [70] dplyr_0.4.3 > [71] rtracklayer_1.32.1 > [72] KernSmooth_2.23-15 > [73] stringi_1.1.1 > [74] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 > [75] BatchJobs_1.6 > [76] Rcpp_0.12.7 > [77] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 > [78] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 > > > > ------------------------------ > > Post tags: chipqc, ChIPQC > > You may reply via email or visit ChIPQC GRCh38 usage yields "Unsupported annotation:hg38" >
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Hi Coby, Having looked through it seems there was a reference to a non existent hg20 package which I have fixed to hg38. So hg38 is now available in 1.8.7 in current release. Best Tom On Wednesday, 14 September 2016, Thomas Carroll [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Thomas Carroll <https: support.bioconductor.org="" u="" 7019=""/> wrote Answer: > ChIPQC GRCh38 usage yields "Unsupported annotation:hg38" > <https: support.bioconductor.org="" p="" 87096="" #87116="">: > > hi Coby, Yes, GRCh38 is not supported explicitly in the current release > but I intend to add to next Bioconductor release. You can however add any > annotation you wish to ChIPQC using the methods discussed in this thread. creating > custom genome annotation for the ChIPQC package > <https: support.bioconductor.org="" p="" 70893=""/> If you can't wait for > upcoming release (I believe end of October) I can also provide the > annotation off-list if you email directly and again you can provide this to > ChIPQC as described in thread above. best, tom On Wed, Sep 14, 2016 at 7:14 > PM, Coby Viner [bioc] <noreply@bioconductor.org> <javascript:_e(%7b%7d,'cvml','noreply@bioconductor.org');>> wrote: > > Activity on a post you are following on support.bioconductor.org > > User > Coby Viner <https: support.bioconductor.org="" u="" 10939=""/> wrote > Question: > ChIPQC GRCh38 usage yields "Unsupported annotation:hg38" > > <https: support.bioconductor.org="" p="" 87096=""/>: > > I am unable to > use ChIPQC with GRCh38/hg38. When I attempt to, via experiment > <- > ChIPQC(samples, annotation="hg38"), I obtain: > > Compiling annotation... > > Error in getAnnotation(annotation, AllChr = chromosomes) : > Unsupported > annotation:hg38 > Calls: ChIPQC -> getAnnotation > > > ------------------------------ > > > > > sessionInfo() > R version 3.3.0 > (2016-05-03) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: > CentOS release 6.3 (Final) > > locale: > [1] LC_CTYPE=en_US.UTF-8 > LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] > LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 > LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] > LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > > [1] stats4 parallel stats graphics grDevices utils datasets > [8] methods > base > > other attached packages: > [1] ChIPQC_1.8.5 DiffBind_2.0.2 > [3] > SummarizedExperiment_1.2.3 Biobase_2.32.0 > [5] GenomicRanges_1.24.2 > GenomeInfoDb_1.8.1 > [7] IRanges_2.6.1 S4Vectors_0.10.1 > [9] > BiocGenerics_0.18.0 ggplot2_2.1.0 > [11] BiocInstaller_1.22.3 > > loaded > via a namespace (and not attached): > [1] edgeR_3.14.0 > [2] splines_3.3.0 > > [3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 > [4] > TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 > [5] gtools_3.5.0 > [6] > assertthat_0.1 > [7] latticeExtra_0.6-28 > [8] amap_0.8-14 > [9] > RBGL_1.48.1 > [10] Rsamtools_1.24.0 > [11] Category_2.38.0 > [12] > RSQLite_1.0.0 > [13] backports_1.0.2 > [14] lattice_0.20-33 > [15] > limma_3.28.10 > [16] digest_0.6.10 > [17] RColorBrewer_1.1-2 > [18] > XVector_0.12.0 > [19] checkmate_1.8.0 > [20] colorspace_1.2-6 > [21] > Matrix_1.2-6 > [22] plyr_1.8.4 > [23] GSEABase_1.34.0 > [24] chipseq_1.22.0 > > [25] XML_3.98-1.4 > [26] pheatmap_1.0.8 > [27] ShortRead_1.30.0 > [28] > biomaRt_2.28.0 > [29] genefilter_1.54.2 > [30] zlibbioc_1.18.0 > [31] > xtable_1.8-2 > [32] GO.db_3.3.0 > [33] scales_0.4.0 > [34] brew_1.0-6 > > [35] gdata_2.17.0 > [36] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 > [37] > BiocParallel_1.6.2 > [38] annotate_1.50.0 > [39] GenomicFeatures_1.24.2 > > [40] survival_2.39-4 > [41] magrittr_1.5 > [42] systemPipeR_1.6.2 > [43] > fail_1.3 > [44] gplots_3.0.1 > [45] hwriter_1.3.2 > [46] GOstats_2.38.0 > > [47] graph_1.50.0 > [48] tools_3.3.0 > [49] BBmisc_1.9 > [50] stringr_1.1.0 > > [51] sendmailR_1.2-1 > [52] munsell_0.4.3 > [53] locfit_1.5-9.1 > [54] > AnnotationDbi_1.34.3 > [55] Biostrings_2.40.2 > [56] caTools_1.17.1 > [57] > grid_3.3.0 > [58] RCurl_1.95-4.8 > [59] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 > > [60] rjson_0.2.15 > [61] AnnotationForge_1.14.2 > [62] bitops_1.0-6 > > [63] base64enc_0.1-3 > [64] gtable_0.2.0 > [65] DBI_0.4-1 > [66] > reshape2_1.4.1 > [67] R6_2.1.3 > [68] GenomicAlignments_1.8.3 > [69] > Nozzle.R1_1.1-1 > [70] dplyr_0.4.3 > [71] rtracklayer_1.32.1 > [72] > KernSmooth_2.23-15 > [73] stringi_1.1.1 > [74] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 > > [75] BatchJobs_1.6 > [76] Rcpp_0.12.7 > [77] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 > > [78] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 > > > > > ------------------------------ > > Post tags: chipqc, ChIPQC > > You may > reply via email or visit ChIPQC GRCh38 usage yields "Unsupported > annotation:hg38" <https: support.bioconductor.org="" p="" 87096=""/> > > > ------------------------------ > > Post tags: chipqc, ChIPQC > > You may reply via email or visit https://support.bioconductor. > org/p/87096/#87116 >
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Thanks for fixing this!

I am now able to call ChIPQC with annotation="hg38", but I now receive an error later in the pipeline, during ChIPQCreport(experiment), after successfully obtaining the result of QCmetrics(experiment), and after the generation of ChIPQCreport/CCPlot.png (but no other files).

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Hi Coby, Could you save a copy of the chipqcexperiment object as an RData file and send privately? If it is a problem useful to others we will open a new issue and post solution. Best Tom On Friday, 23 September 2016, Coby Viner [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Coby Viner <https: support.bioconductor.org="" u="" 10939=""/> wrote Comment: > ChIPQC GRCh38 usage yields "Unsupported annotation:hg38" > <https: support.bioconductor.org="" p="" 87096="" #87397="">: > > Thanks for fixing this! > > I am now able to call ChIPQC with annotation="hg38", but I now receive an > error later in the pipeline, during ChIPQCreport(experiment), after > successfully obtaining the result of QCmetrics(experiment), and after the > generation of ChIPQCreport/CCPlot.png (but no other files). > > ------------------------------ > > Post tags: chipqc, ChIPQC > > You may reply via email or visit https://support.bioconductor. > org/p/87096/#87397 >
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We have determined off-list that this new error had nothing to do with the GRCh38 annotation, but was due to ChIPQC's need for a "Replicate" to be defined for every sample. See: ChIPQCreport yields a cryptic error if "Replicate" data is not specified.

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