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