Chapter 6 Output

6.1 QuickOmics visualization

The output results can be piped to QuickOmics (http://quickomics.bxgenomics.com) for visualization. Here are the four necessary files required by QuickOmics:

SRP199678_estCount.rds

SRP199678_network.RData

SRP199678.RData

SRP199678.csv

This example has been uploaded to the QuickOmics site:

https://quickomics.bxgenomics.com/?serverfile=SRP199678

6.2 Other output files

Also, the EA pipeline generates a couple of files under the working directory.

The pdf files and index.html can be directly visualized by the user. However, we suggest the user download the ready-to-transfer ProjectName_BookdownReport.tar.gz tarball and open the index.html file inside for visualization.

Here is an example of the output directory hierarchy:

SRP199678/
    ├── comparison.csv
    ├── counts.tsv
    ├── EA20220328_0                       #This directory was generated by the EA pipeline
      ├── BookdownReport/
        ├── ...
        ├── docs/
          ├── index.html                   #Original bookdown report
          └── ....
      ├── config.yml
      ├── data/
      ├── notAdjusted_Covariate_PC_Results.rds
      ├── notAdjusted_Covariate_PC_Results.xlsx
      ├── notAdjusted_PCA_Plots.pdf
      ├── notAdjusted_Significant_Categorical_Covariates.pdf
      ├── notAdjusted_Significant_Numeric_Covariates.pdf
      ├── sequenceQC.pdf
      ├── sequenceQC.unionTop.TPM.csv
      ├── session.EAinit                   #Four R sessionInfo() outputs
      ├── session.EAqc
      ├── session.EAreport
      ├── session.EArun
      ├── SRP199678_BookdownReport.tar.gz  #Bookdown report tarball
      ├── SRP199678.csv                    #QuickOmics file 1
      ├── SRP199678_estCount.rds           #QuickOmics file 2
      ├── SRP199678_network.RData          #QuickOmics file 3
      ├── SRP199678.RData                  #QuickOmics file 4
    ├── geneAnnotation.csv
    ├── geneLength.tsv
    ├── meta.csv
    └── project.yml