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Can Alevin tool be made to work with GTF from Gencode please?
When walking through the Alevin tutorial (https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/droplet-quantification-preprocessing/tutorial.html) on the Human transcriptome "Comprehensive gene annotation" GTF file from Gencode (https://www.gencodegenes.org/human/) on the usegalaxy.eu server, the GTF2GeneList tools fails when the "Flag Mitochondrial Features" option is enabled (default parameters) with this error:
Error in [[<-(tmp, name, value = character(0)) :
0 elements in value to replace 258145 elements
Calls: $<- -> $<- -> [[<- -> [[<-
Execution halted
I tried the GTF with or without the "scaffolds, assembly patches and alternate loci" with the same error. Am I missing something or is this an actual bug? It seems to work fine on genes and transcripts but adding the mito features always makes it crash.
The text was updated successfully, but these errors were encountered:
Can Alevin tool be made to work with GTF from Gencode please?
When walking through the Alevin tutorial (https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/droplet-quantification-preprocessing/tutorial.html) on the Human transcriptome "Comprehensive gene annotation" GTF file from Gencode (https://www.gencodegenes.org/human/) on the usegalaxy.eu server, the GTF2GeneList tools fails when the "Flag Mitochondrial Features" option is enabled (default parameters) with this error:
Error in [[<-(tmp, name, value = character(0)) :
0 elements in value to replace 258145 elements
Calls: $<- -> $<- -> [[<- -> [[<-
Execution halted
I tried the GTF with or without the "scaffolds, assembly patches and alternate loci" with the same error. Am I missing something or is this an actual bug? It seems to work fine on genes and transcripts but adding the mito features always makes it crash.
The text was updated successfully, but these errors were encountered: