HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 annotation
Entering edit mode
Yue • 0
Last seen 9 months ago
Hong Kong

Hi, dear authors, Thanks for developing this tool. I encountered an issue with construct_features part during testing.

> construct_features(output_path=paste0(outdir,"/CHM13_50kb_GATC"),
+                    gen="Hsapiens",gen_ver="T2T.CHM13v2.0",
+                    sig="GATC",bin_type="Bins-uniform",
+                    binsize=50000,
+                    chrs=c("chr21","chr22"))
Error in library(genome, character.only = TRUE) : 

sessionInfo( )
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

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

other attached packages:
 [1] BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0 BSgenome.Hsapiens.UCSC.hg19_1.4.3         
 [3] BSgenome_1.66.1                            rtracklayer_1.58.0                        
 [5] Biostrings_2.66.0                          XVector_0.38.0                            
 [7] GenomicRanges_1.50.1                       GenomeInfoDb_1.34.3                       
 [9] IRanges_2.32.0                             S4Vectors_0.36.0                          
[11] BiocGenerics_0.44.0                        HiCDCPlus_1.6.0                           

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3            rjson_0.2.21                deldir_1.0-6               
  [4] ellipsis_0.3.2              biovizBase_1.46.0           htmlTable_2.4.1            
  [7] base64enc_0.1-3             dichromat_2.0-0.1           rstudioapi_0.14            
 [10] farver_2.1.1                bit64_4.0.5                 AnnotationDbi_1.60.0       
 [13] fansi_1.0.3                 xml2_1.3.3                  codetools_0.2-18           
 [16] splines_4.2.2               R.methodsS3_1.8.2           cachem_1.0.6               
 [19] geneplotter_1.76.0          knitr_1.41                  Formula_1.2-4              
 [22] Rsamtools_2.14.0            annotate_1.76.0             cluster_2.1.4              
 [25] dbplyr_2.2.1                png_0.1-7                   R.oo_1.25.0                
 [28] BiocManager_1.30.19         compiler_4.2.2              httr_1.4.4                 
 [31] backports_1.4.1             lazyeval_0.2.2              assertthat_0.2.1           
 [34] Matrix_1.5-1                fastmap_1.1.0               cli_3.4.1                  
 [37] htmltools_0.5.3             prettyunits_1.1.1           tools_4.2.2                
 [40] igraph_1.3.5                gtable_0.3.1                glue_1.6.2                 
 [43] GenomeInfoDbData_1.2.9      dplyr_1.0.10                rappdirs_0.3.3             
 [46] Rcpp_1.0.9                  Biobase_2.58.0              vctrs_0.5.1                
 [49] xfun_0.35                   stringr_1.4.1               lifecycle_1.0.3            
 [52] ensembldb_2.22.0            restfulr_0.0.15             XML_3.99-0.12              
 [55] InteractionSet_1.26.0       MASS_7.3-58.1               zlibbioc_1.44.0            
 [58] scales_1.2.1                VariantAnnotation_1.44.0    ProtGenerics_1.30.0        
 [61] GenomicInteractions_1.32.0  hms_1.1.2                   MatrixGenerics_1.10.0      
 [64] parallel_4.2.2              SummarizedExperiment_1.28.0 AnnotationFilter_1.22.0    
 [67] RColorBrewer_1.1-3          yaml_2.3.6                  curl_4.3.3                 
 [70] memoise_2.0.1               gridExtra_2.3               ggplot2_3.4.0              
 [73] biomaRt_2.54.0              rpart_4.1.19                latticeExtra_0.6-30        
 [76] stringi_1.7.8               RSQLite_2.2.18              BiocIO_1.8.0               
 [79] checkmate_2.1.0             GenomicFeatures_1.50.2      filelock_1.0.2             
 [82] BiocParallel_1.32.3         rlang_1.0.6                 pkgconfig_2.0.3            
 [85] matrixStats_0.63.0          bitops_1.0-7                lattice_0.20-45            
 [88] purrr_0.3.5                 labeling_0.4.2              GenomicAlignments_1.34.0   
 [91] htmlwidgets_1.5.4           bit_4.0.5                   tidyselect_1.2.0           
 [94] DESeq2_1.38.1               magrittr_2.0.3              R6_2.5.1                   
 [97] generics_0.1.3              Hmisc_4.7-2                 DelayedArray_0.24.0        
[100] DBI_1.1.3                   pillar_1.8.1                foreign_0.8-83             
[103] withr_2.5.0                 survival_3.4-0              KEGGREST_1.38.0            
[106] RCurl_1.98-1.9              nnet_7.3-18                 tibble_3.1.8               
[109] crayon_1.5.2                interp_1.1-3                utf8_1.2.2                 
[112] BiocFileCache_2.6.0         jpeg_0.1-9                  progress_1.2.2             
[115] locfit_1.5-9.6              grid_4.2.2                  data.table_1.14.6          
[118] blob_1.2.3                  digest_0.6.30               xtable_1.8-4               
[121] tidyr_1.2.1                 R.utils_2.12.2              munsell_0.5.0              
[124] Gviz_1.42.0                

Sorry about the default language of Rstudio. It means There is no package named 'BSgenome.Hsapiens.UCSC.T2T.CHM13v2.0' The BSgenome has no BSgenome.Hsapiens.UCSC.T2T.CHM13v2.0 but BSgenome.Hsapiens.NCBI.T2T.CHM13v2.08 currently. Are there any ways for me to use NCBI assembly rather than UCSC during constructing features procedure? Sincerely Gemma

HiC-DC+ HiCDCPlus • 297 views
Entering edit mode

Hi @Gemma-Zhang-326 , the package currently runs only on genomes and versions with UCSC annotations. I will need to issue an update to use NCBI annotations. In the meantime, you can clone a copy from this repo, change the ".UCSC" coding in the following files to ".NCBI" get_chrs.R construct_features.R get_enzyme_cutsites.R get_chr_sizes.R and install package from source:

install.packages(path_to_the_cloned_and_edited_folder, repos = NULL, type="source")

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