The output will look a little something... like this:

• {Gene Name} - is hopefully self explanatory.
  • plots - contains the *.html and *.png outputs of your visualisation.
  • resources - contains the STAR alignments, the assembly, reference GTF, and superTranscript fasta.
  • temp - Only necessary if you want to rerun bpipe without losing any progress. Feel free to delete.
• Log.out - Bpipe's log file
• .bpipe - Bpipe's inner workings
• commandlog.txt - The commands that .bpipe ran.