Error in .merge_transcript_parts(transcripts)
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Entering edit mode
csijcs • 0
@csijcs-18327
Last seen 2.5 years ago

Hello,

I am trying to make a txdb from a .gff of sncRNA obtained from the DASHR database (DASHR v2.0 hg38 sncRNA annotation [GFF]). I had to do a little formatting to remove the 10th column of some lines, but once that was done I tried importing and making a txdb with makeTxDbFromGFF and receive the following error:

>TxDb <- makeTxDbFromGFF(file = "/data2/csijcs/hg38/dashr.v2.sncRNA.annotation.hg38.edited.gff", format="auto")
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in .merge_transcript_parts(transcripts) : 
  The following transcripts have multiple parts that cannot be merged
  because of incompatible type: U13, U3, U8

I tried removing those lines, but got even more errors:

> TxDb <- makeTxDbFromGFF(file = "/data2/csijcs/hg38/dashr.v2.sncRNA.annotation.hg38.edited.noU13U3U6U8.gff", format="auto")
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in .merge_transcript_parts(transcripts) : 
  The following transcripts have multiple parts that cannot be merged
  because of incompatible seqnames: 5S, LSU-rRNA_Hsa, SSU-rRNA_Hsa, U1,
  U14, U17, U2, U4, U5, U6, U7

 

Is it possible to make a TxDb for this annotation file?  I am trying to perform differential expression with DESeq.

Here is my sessionInfo:

> sessionInfo() 
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/csijcs/anaconda2/lib/R/lib/libRblas.so
LAPACK: /home/csijcs/anaconda2/lib/R/lib/libRlapack.so

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] rtracklayer_1.40.6                     
 [2] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
 [3] apeglm_1.2.1                           
 [4] tximportData_1.8.0                     
 [5] readr_1.1.1                            
 [6] tximport_1.8.0                         
 [7] RColorBrewer_1.1-2                     
 [8] ggplot2_3.1.0                          
 [9] DESeq2_1.20.0                          
[10] SummarizedExperiment_1.10.1            
[11] DelayedArray_0.6.6                     
[12] BiocParallel_1.14.2                    
[13] matrixStats_0.54.0                     
[14] GenomicFeatures_1.32.3                 
[15] AnnotationDbi_1.42.1                   
[16] Biobase_2.40.0                         
[17] GenomicRanges_1.32.7                   
[18] GenomeInfoDb_1.16.0                    
[19] IRanges_2.14.12                        
[20] S4Vectors_0.18.3                       
[21] BiocGenerics_0.26.0                    

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             mirbase.db_1.2.0         bit64_0.9-7             
 [4] progress_1.2.0           httr_1.3.1               numDeriv_2016.8-1       
 [7] tools_3.5.0              backports_1.1.2          R6_2.3.0                
[10] rpart_4.1-13             Hmisc_4.1-1              DBI_1.0.0               
[13] lazyeval_0.2.1           colorspace_1.3-2         nnet_7.3-12             
[16] withr_2.1.2              tidyselect_0.2.5         gridExtra_2.3           
[19] prettyunits_1.0.2        bit_1.1-14               compiler_3.5.0          
[22] htmlTable_1.12           scales_1.0.0             checkmate_1.8.5         
[25] genefilter_1.62.0        stringr_1.3.1            digest_0.6.18           
[28] Rsamtools_1.32.3         foreign_0.8-71           XVector_0.20.0          
[31] base64enc_0.1-3          pkgconfig_2.0.2          htmltools_0.3.6         
[34] bbmle_1.0.20             htmlwidgets_1.3          rlang_0.3.0.1           
[37] rstudioapi_0.8           RSQLite_2.1.1            bindr_0.1.1             
[40] acepack_1.4.1            dplyr_0.7.8              RCurl_1.95-4.11         
[43] magrittr_1.5             GenomeInfoDbData_1.1.0   Formula_1.2-3           
[46] Matrix_1.2-15            Rcpp_1.0.0               munsell_0.5.0           
[49] stringi_1.2.4            MASS_7.3-51.1            zlibbioc_1.26.0         
[52] plyr_1.8.4               grid_3.5.0               blob_1.1.1              
[55] crayon_1.3.4             lattice_0.20-38          Biostrings_2.48.0       
[58] splines_3.5.0            annotate_1.58.0          hms_0.4.2               
[61] locfit_1.5-9.1           knitr_1.20               pillar_1.3.0            
[64] geneplotter_1.58.0       biomaRt_2.36.1           XML_3.98-1.16           
[67] glue_1.3.0               latticeExtra_0.6-28      data.table_1.11.8       
[70] BiocManager_1.30.4       gtable_0.2.0             purrr_0.2.5             
[73] assertthat_0.2.0         emdbook_1.3.10           xtable_1.8-3            
[76] coda_0.19-2              survival_2.43-1          tibble_1.4.2            
[79] GenomicAlignments_1.16.0 memoise_1.1.0            bindrcpp_0.2.2          
[82] cluster_2.0.7-1         
 

maketxdbfromgff • 527 views
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Entering edit mode

I've tested this with a modified file (10th column removed since GFF files have 9 columns), and got the same error as you. The error is thrown by the .merge_transcript_parts() function in GenomicFeatures. In essence, tt seems the reason you are getting the error is that the tx_type value generated in the function from the ID=<something> 9th column in your file contains values that are not unique (e.g. ID=U4 is not unique). To get maketxdbdbfromgff() to work, it seems that you need to make all of the 9th columns values in your gff file unique, or remove non-unique columns.
 

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