yeah, it's the gene_id/transcript_id being the same value in UCSC GTFs. I know why the TB outputs the data that way but many people completely miss it .. and then get odd results --since the counts are really by transcript, not gene :(
either way I added a small comment to biostar, feel free to accept the answer :)
Oh! I found the tools at usegalaxy.eu. Not sure how I missed those in the MTS! I'll point the user to the other server. Tx!
Is it possible in 18.01 to run tools on subsets of collections, or to "explode"/"eject" collections into individual history items?
You can drag and drop individual items into the tool form - if you have a more systematic way to indentify the elements there is also a tool that filters a collection from a tabular file - this isn’t super straight forward but it enables a high level of tracking and use within workflows
There isn’t an explode tool though in 18.05
I meant 18.01
Does anyone know if Deseq2 in Galaxy can be configured to run with single-end data? Or is paired-end input required?
paired end is not required
DeSeq2 is only taking counts and don't care about single/paired
Ok, there must be something else wrong with the inputs. Another bug report had the same error message and paired end inputs were used. There was only one replicate per condition in that example - maybe the counts are too sparse to do the DE.
whomever implemented the sort flag for tool test outputs, I owe you a beer