IsoformSwitchAnalyzeR package on mouse data
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Entering edit mode
Ryan • 0
@d6139ae0
Last seen 4 months ago
United States

I am trying to use IsoformSwitchAnalyzeR package to assess Isoform switching on mouse RNA seq data. I am running into problems on the GTF file that it needs to read in order to perform the analysis. I am not able to find the ensembl file that has haplotype info in it. Does anyone know where I can find this or how I would proceed using IsoformSwitchAnalyzeR without the "chr_patch_hapl_scaff.gtf" file.

Per my code below on the 'isoformExonAnnoation', I can only locate the 'Mus_musculus.GRCm39.107.chr.gtf' file, which it does not like and will not read in.


mySwitchList <- importRdata(
  isoformCountMatrix   = Txi_trans$counts,
  isoformRepExpression = Txi_trans$abundance,
  designMatrix         = targets.mod,
  removeNonConvensionalChr = TRUE,
  addAnnotatedORFs=TRUE,
  ignoreAfterPeriod=TRUE,
  isoformExonAnnoation = "Mus_musculus.GRCm39.107.chr.gtf",
  isoformNtFasta       = "Mus_musculus.GRCm39.cdna.all.fa",
  showProgress = TRUE)


sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] IsoformSwitchAnalyzeR_1.18.0 DEXSeq_1.42.0                RColorBrewer_1.1-3          
 [4] DESeq2_1.36.0                SummarizedExperiment_1.26.1  MatrixGenerics_1.8.1        
 [7] BiocParallel_1.30.3          gt_0.6.0                     plotly_4.10.0               
[10] DT_0.23                      cowplot_1.1.1                matrixStats_0.62.0          
[13] edgeR_3.38.1                 limma_3.52.2                 beepr_1.3                   
[16] EnsDb.Mmusculus.v79_2.99.0   ensembldb_2.20.2             AnnotationFilter_1.20.0     
[19] GenomicFeatures_1.48.3       AnnotationDbi_1.58.0         Biobase_2.56.0              
[22] GenomicRanges_1.48.0         GenomeInfoDb_1.32.2          IRanges_2.30.0              
[25] S4Vectors_0.34.0             BiocGenerics_0.42.0          tximport_1.24.0             
[28] forcats_0.5.1                stringr_1.4.0                dplyr_1.0.9                 
[31] purrr_0.3.4                  readr_2.1.2                  tidyr_1.2.0                 
[34] tibble_3.1.8                 ggplot2_3.3.6                tidyverse_1.3.2             
[37] rhdf5_2.40.0                 BiocManager_1.30.18         

loaded via a namespace (and not attached):
  [1] readxl_1.4.0                  backports_1.4.1               AnnotationHub_3.4.0          
  [4] DRIMSeq_1.24.0                BiocFileCache_2.4.0           plyr_1.8.7                   
  [7] lazyeval_0.2.2                tximeta_1.14.1                splines_4.2.0                
 [10] crosstalk_1.2.0               digest_0.6.29                 htmltools_0.5.3              
 [13] fansi_1.0.3                   magrittr_2.0.3                checkmate_2.1.0              
 [16] memoise_2.0.1                 BSgenome_1.64.0               googlesheets4_1.0.0          
 [19] tzdb_0.3.0                    annotate_1.74.0               Biostrings_2.64.0            
 [22] modelr_0.1.8                  vroom_1.5.7                   prettyunits_1.1.1            
 [25] colorspace_2.0-3              blob_1.2.3                    rvest_1.0.2                  
 [28] rappdirs_0.3.3                haven_2.5.0                   crayon_1.5.1                 
 [31] RCurl_1.98-1.7                jsonlite_1.8.0                hexbin_1.28.2                
 [34] genefilter_1.78.0             survival_3.3-1                glue_1.6.2                   
 [37] gtable_0.3.0                  gargle_1.2.0                  zlibbioc_1.42.0              
 [40] XVector_0.36.0                DelayedArray_0.22.0           Rhdf5lib_1.18.2              
 [43] scales_1.2.0                  futile.options_1.0.1          DBI_1.1.3                    
 [46] Rcpp_1.0.9                    xtable_1.8-4                  viridisLite_0.4.0            
 [49] progress_1.2.2                bit_4.0.4                     htmlwidgets_1.5.4            
 [52] httr_1.4.3                    ellipsis_0.3.2                pkgconfig_2.0.3              
 [55] XML_3.99-0.10                 farver_2.1.1                  sass_0.4.2                   
 [58] dbplyr_2.2.1                  locfit_1.5-9.6                utf8_1.2.2                   
 [61] later_1.3.0                   reshape2_1.4.4                tidyselect_1.1.2             
 [64] labeling_0.4.2                rlang_1.0.4                   BiocVersion_3.15.2           
 [67] munsell_0.5.0                 cellranger_1.1.0              tools_4.2.0                  
 [70] cachem_1.0.6                  cli_3.3.0                     generics_0.1.3               
 [73] RSQLite_2.2.15                audio_0.1-10                  broom_1.0.0                  
 [76] fastmap_1.1.0                 yaml_2.3.5                    bit64_4.0.5                  
 [79] fs_1.5.2                      KEGGREST_1.36.3               nlme_3.1-158                 
 [82] mime_0.12                     formatR_1.12                  xml2_1.3.3                   
 [85] biomaRt_2.52.0                compiler_4.2.0                rstudioapi_0.13              
 [88] interactiveDisplayBase_1.34.0 filelock_1.0.2                curl_4.3.2                   
 [91] png_0.1-8                     reprex_2.0.1                  statmod_1.4.36               
 [94] geneplotter_1.74.0            bslib_0.4.0                   stringi_1.7.8                
 [97] futile.logger_1.4.3           lattice_0.20-45               ProtGenerics_1.28.0          
[100] Matrix_1.4-1                  vctrs_0.4.1                   pillar_1.8.0                 
[103] lifecycle_1.0.1               rhdf5filters_1.8.0            jquerylib_0.1.4              
[106] data.table_1.14.2             bitops_1.0-7                  httpuv_1.6.5                 
[109] rtracklayer_1.56.1            hwriter_1.3.2.1               R6_2.5.1                     
[112] BiocIO_1.6.0                  promises_1.2.0.1              gridExtra_2.3                
[115] sessioninfo_1.2.2             codetools_0.2-18              lambda.r_1.2.4               
[118] MASS_7.3-58                   assertthat_0.2.1              rjson_0.2.21                 
[121] withr_2.5.0                   GenomicAlignments_1.32.1      Rsamtools_2.12.0             
[124] GenomeInfoDbData_1.2.8        mgcv_1.8-40                   parallel_4.2.0               
[127] hms_1.1.1                     VennDiagram_1.7.3             grid_4.2.0                   
[130] googledrive_2.0.0             shiny_1.7.2                   lubridate_1.8.0              
[133] restfulr_0.0.15
rnaseq IsoformSwitchAnalyzeR • 258 views
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Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem?

Best

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Which version of Ensembl are you using?

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