- In your analyses folder, click on "HTSeq-count-0.6.1"
- 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
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.
- Move all your paired.sorted.XXX.txt files to one folder for the easiest analysis
- 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)
- Need to create a target file: Refer to https://pods.iplantcollaborative.org/wiki/pages/viewpage.action?pageId=28115144b look below for image
- Reference Biological condition: probably whatever the name is for your untreated/control samples
- Everything else: as default
Output File Types:
- In your analyses folder, click on "Deseq2(multifactorial pairwise comparison)"
- You will see "XXX.complete.txt" which has all the genes and your pairwise comparison
- You will see "XXX.up.txt" are genes that are upregulated in your pairwise comoparison
- You will see "XXX.down.txt" are genes that are downregulated in your pairwise comparison