This space is home to learning materials and tutorials created for CyVerse products and services. To search the entire CyVerse wiki, use the box at the upper right.





Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


  1. In your analyses folder, click on "HTSeq-count-0.6.1" 
  2. You will see "paired.sorted.XXXX.txt" files for your counts . This will be your count matrix

Example of Count Matrix for UT_top5M_1.sorted

Image Added


Now that we know the quantity of each transcript in each sample we need to compare those quantities between samples. For this we will use DESeq2.


  1. Move all your paired.sorted.XXX.txt files to one folder for the easiest analysis
  2. Select all your paired.sorted.XXX.txt files for your input (you can not do 27 pairwise at the same time, select smaller sets of samples for your pairwise comparisons)
  3. Need to create a target file: Refer to look below for image
  4. Select:
    1. Reference Biological condition: probably whatever the name is for your untreated/control samples
    2. Everything else: as default

Image Added

Output File Types:

  1. In your analyses folder, click on "Deseq2(multifactorial pairwise comparison)" 
  2. You will see "XXX.complete.txt" which has all the genes and your pairwise comparison
  3. You will see "XXX.up.txt" are genes that are upregulated in your pairwise comoparison
  4. You will see "XXX.down.txt" are genes that are downregulated in your pairwise comparison