Trouble with detecting AS events using ASpediaFI
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@rezashiralmohammad-21811
Last seen 24 days ago
Iran

Hi,

Looking for a package to investigate the functional interactions of alternative splicing events, I found "ASpediaFI" on Bioconductor. Although I successfully performed the analysis on trial data, I faced an error when trying to detect and annotate AS events from the actual hg38 GTF file.

I would be appreciated it if someone could tell me where the problem is?

The code I have used is:

#Detect and annotate AS events from a subset of the hg38 GTF file
gtf <- "Homo_sapiens.GRCh38.104.gtf"
SF1.ASpediaFI <- annotateASevents(SF1.ASpediaFI,
                                        gtf.file = gtf, num.cores = 40)

I have faced the following error:

Error in each.chr.txTable[, "GENEID"] : incorrect number of dimensions
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Attaching SeuratObject

And my sessionInfo is as follow:

> sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
 [1] igraph_1.2.11               ASpediaFI_1.8.0            
 [3] ROCR_1.0-11                 AnnotationHub_3.2.2        
 [5] BiocFileCache_2.2.1         dbplyr_2.1.1               
 [7] sva_3.42.0                  BiocParallel_1.28.3        
 [9] mgcv_1.8-38                 nlme_3.1-152               
[11] data.table_1.14.2           limma_3.50.1               
[13] gplots_3.1.1                pheatmap_1.0.12            
[15] ggrepel_0.9.1               genefilter_1.76.0          
[17] DESeq2_1.34.0               forcats_0.5.1              
[19] stringr_1.4.0               purrr_0.3.4                
[21] readr_2.1.2                 tidyr_1.2.0                
[23] tibble_3.1.6                tidyverse_1.3.1            
[25] plotrix_3.8-2               Matrix_1.4-0               
[27] GeomxTools_2.0.0            NanoStringNCTools_1.2.0    
[29] SingleCellExperiment_1.16.0 glmGamPoi_1.6.0            
[31] RColorBrewer_1.1-2          celldex_1.4.0              
[33] dplyr_1.0.8                 SingleR_1.8.1              
[35] SummarizedExperiment_1.24.0 Biobase_2.54.0             
[37] GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
[39] IRanges_2.28.0              S4Vectors_0.32.4           
[41] BiocGenerics_0.40.0         MatrixGenerics_1.6.0       
[43] matrixStats_0.61.0          ggplot2_3.3.5              
[45] SeuratObject_4.0.4          Seurat_4.1.0               
ASpediaFI • 110 views
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@660f9f1a
Last seen 28 days ago
South Korea

Assuming you downloaded "Homo_sapiens.GRCh38.104.gtf" from the Ensembl website, the gene model contains reference chromosomes (chr1-22, X, Y, MT) as well as GL000XXX.X and KI270XXX.1. The "annotateASevents" function is based on the R package "IVAS", and it does not support those non-reference genomic regions yet.

Unless you are particularly interested in analyzing AS events in those regions, I would recommend you modify the current gtf file to drop those regions or use another GRCh38 gene model (e.g., https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/gencode.v31.annotation.gtf.gz).

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