Program crashes with a genome with no alternative spliced genes annotated

[christophe...@gmail.com]

Hi.

Firstly great software.

Normally it works perfectly fine. However I am hitting one stumbling block. That is the program keeps crashing for after I hit run for the limma calculation. I will paste the error below. But from what I can tell it is because in the genome I am using no alternative spliced genes are annotated. I am using a published GTF for the genes to transcripts mapping file.

So my question: Is there anyway of getting around this?????

DE gene analysis
Limma-voon to estimate mean-vriance trend ...
Fit a basic linear model ...
Fit the contrast model ...
[1] "Contrast groups: X2-X2.5; X1.5-X2.5; X1-X2.5; X0.5-X2.5; X0.1-X2.5; X12hrREH-X2.5; X24hrREH-X2.5"
Fit a eBayes model ...
Testing for each contrast group ...
Testing across all contrast groups ...
Time for analysis: 4.023
Done!!! 
Generating deltaPS...

DAS gene, DE and DTU transcript analysis
Limma-voon to estimate mean-vriance trend ...
Fit a basic linear model ...
Fit the contrast model ...
[1] "Contrast groups: X2-X2.5; X1.5-X2.5; X1-X2.5; X0.5-X2.5; X0.1-X2.5; X12hrREH-X2.5; X24hrREH-X2.5"
Fit a eBayes model ...
Testing for each contrast group ...
Testing across all contrast groups ...
Fit a splicing model ...
Total number of exons:  20117 
Total number of genes:  20117 
Number of genes with 1 exon:  20117 
Mean number of exons in a gene:  1 
Max number of exons in a gene:  1 
Warning: Error in diffSplice: No genes with more than one exon
  79: stop
  78: diffSplice
  77: limma.pipeline [R/pipeline.R#268]
  73: observeEventHandler [source/server/server_ddd.R#503]
   2: shiny::runApp
   1: run3DApp

[wenbin guo]

Hi,

To perform alternative splicing analysis, you need a transcriptome in which some of the genes have multiple transcripts. In your case, it seems that you only need gene level differential expression analsysi, instead of alternative splicng analysis. Since you are using the command line, you can skip the DAS/DTU analysis step. But the downstream code, you  may need to modify a bit to summarize the gene level results.