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NOT URGENT AT ALL minor issue with Alevin and GTF #234

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nomadscientist opened this issue Jun 4, 2021 · 0 comments
Open

NOT URGENT AT ALL minor issue with Alevin and GTF #234

nomadscientist opened this issue Jun 4, 2021 · 0 comments

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@nomadscientist
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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.

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