The tRNAnalysis report

Before running the report

For the report to run successfully you will need to set up a design file (Actually, you can have multiple design files in there and all will run simultaneously) that controls how the differential expression model and contract will be performed.

The file has the naming convention design_<test>_<control>_<test>_<column>.csv

  • <test> - refers to the test that you plan to run. There are two options “ltr” or “wald”.
  • <control> - This is the name of your control condition i.e. the samples you want to test against. This should match one of the samples within the <column> of the design file.
  • <test> - This is the name of the test condition. This should match with one of the samples in the <column> of the design file
  • <column> - This is a column name that you want to use for your testing in the design_* file

tRNAnalysis runs DEseq2 under the hood so you can refer to the bioconductor help pages for further information on how to set up contrasts for your data.

The design file should be laid out as follows, with the last model column detailing the model that you would like DESeq2 to run for the data.

design layout
Sample condition sample_type model
NORMAL_10KP_2481_miRNA1 k10 cell1 ~condition
NORMAL_PLAC_2373_miRNA1 plac cell1  
NORMAL_PLAC_2433_miRNA1 plac cell2  

Opening the report

Once you have ran the software with the command:

trnanalysis make full


trnanalysis make build_report

a final html report should have been generated.

In order to access this report please open the file called FinalReport.html which will be located within the directory that you ran tRNAnalysis. This should open the report in your preferred browser.

Understanding the report

The report contains a number of tabs at the top that display the analysis performed when the pipeline was ran. All of the report is annotated, which should make understanding the report output easier. However, if there are sections that you feel could be explained better then please raise an issue on github.