I have a short question concerning the Input Parameters of the Tool
plotDEXSeq (Visualization of the per gene DEXSeq results (Galaxy Version 184.108.40.206)):
I am not sure about 2 Input parameters in the following screenshot:
Gene identifier: Which gene identifier should I take? I used StringTie in the upstream analysis, which is why I have only MSTRG.tags for novel isoforms. But when I try to run the tool with a MSTRG.-tag from the list (e.g. MSTRG.9077 in the screenshot above), the output pdf is empty (no error occurring). I tried it with gene names, ensembl_ID from known genes in the list - nothing worked, the output is always empty.
Do you know what is going wrong here?
Specify the primary factor name in the DEXSeqResults object: Just to be sure, should I take what is the name of Factor 1 in my DEXSeq experiment (in this case: Genotype)?