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: $<- -> $<- -> [[<- -> [[<-
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.
Hey GTN Teachers and Trainers! As many of you know, we're hosting the GTN Smörgåsbord 2022 Edition: Tapas! (Or GTN Tapas for short), happening March 14-18, 2021, all timezones (24/7 event)
Do you want to teach something at GTN Tapas? Are you curious what the draft schedule looks like? Want to help out? We've collected all of the information for presenters at this year's event and you might want to join the mailing list
Like last year, this event will be completely online, asynchronous, and based around discussions in Slack. Action Item for Presenters: We have a draft schedule in that page, please check it.
Let us (Saskia, myself, anyone from wg-GOAT) know if you have any questions!
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