IsoformSwitchAnalyzeR package on mouse data
Entering edit mode
Ryan • 0
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,
  isoformExonAnnoation = "Mus_musculus.GRCm39.107.chr.gtf",
  isoformNtFasta       = "Mus_musculus.GRCm39.cdna.all.fa",
  showProgress = TRUE)


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

[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
Entering edit mode

Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem?


Entering edit mode

Which version of Ensembl are you using?


Login before adding your answer.

Traffic: 597 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6