Here we discuss the folder schemes I will be using/creating throughout this tutorial. There are two parts to this scheme -- one on Pegasus, and one on your workstation (presumed to be Windows-based) for the final steps of the gene-level analysis

Gene Level Analysis Scheme

Pegasus Folder scheme (for gene-level analysis):

Note: the tilde (~) symbol stands for HOME on unix systems. It basically is the location '/nethome/yourUserName'

• ~/RNASeq/
  • GRCh38/
  • GRCm38/
  • thisProject/
    • FastQFiles/
    • Control1/
    • Control2/
    • Control3/
    • Experimental1/
    • Experimental2/
    • Experimental3/
    • ReadCounts/

Personal Workstation Folder scheme (for gene-level analysis):

• C:\RNASeq\
  • ReadCounts\
  • DESeq2Output\
  • DESeq2DEGenes\
  • EdgeROutput\
  • EdgeRDEGenes\

Isoform Level Analysis Scheme

Pegasus Folder scheme (for isoform-level analysis):

• ~/RNASeq/
  • GRCh38/
  • GRCm38/
  • thisProject/
    • FastQFiles/
    • cuffcompare/
    • cuffdiff/
    • cuffnorm/
    • Control1/
      • cufflinks/
      • cuffquant/
    • Control2/
      • cufflinks/
      • cuffquant/
    • Control3/
      • cufflinks/
      • cuffquant/
    • Experimental1/
      • cufflinks/
      • cuffquant/
    • Experimental2/
      • cufflinks/
      • cuffquant/
    • Experimental3/
      • cufflinks/
      • cuffquant/

Personal Workstation Folder scheme (for isoform-level analysis):

• C:\RNASeq\
  • cuffdiff\
  • cuffnorm\
  • processedCufflinksOutput\
  • CufflinksDEIsoforms\