O) Combine counts

Combine counts (app: Join multiple tab-delimited files)

Description: The Join multiple tab-delimited files app combines the data into one table to serve as input for the next section, the identification of differentially expressed sequences. Documentation: https://pods.iplantcollaborative.org/wiki/display/DEapps/Join+multiple+tab-delimited+files.

1. Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
2. Rename each cutWrapper_output.txt file from the previous section (Trim count tables) so that each file has a unique name. Check the box next to the file name in the Data window, then use the Edit pull-down menu above to select Rename (Sample data: adjust the names to cutWrapper_outputc01.txt (for control), cutWrapper_outputd01.txt (for dehydration), etc).
3. Open the Join multiple tab-delimited files (Public Applications > Experimental > MaizeRNAseq > Join multiple tab-delimited files).
   1. Change 'Analysis Name' to Combine_Counts, add a 'Description' (optional), and use the default 'output folder'.
4. Click on the Parameters tab.
   1. Enter each renamed file into the window labeled Select tab-delimited files. Enter the renamed files in a logical sequence (Sample data: cutWrapper_outputc01.txt, cutWrapper_outputc02.txt, cutWrapper_outputc03.txt, cutWrapper_outputd01.txt, cutWrapper_outputd02.txt, cutWrapper_outputd03.txt). This order determines the sequence of columns in the joined table (Community Data > iplant_training > rna-seq_without_genome > O_combine_counts).
5. Click on "Launch Analysis".
6. Click on 'Analyses' from the DE workspace and monitor the 'Status' of the analysis (e.g., Idle, Submitted, Pending, Running, Completed, Failed).
   1. Once launched, an analysis will continue whether the user remains logged in or not.
   2. Email notifications update on the analysis progress; they can be switched off under 'Preferences'.
   3. If the analysis fails or does not proceed in the anticipated timeline, check these tips for troubleshooting. (Using the sample data, the analysis should be complete in less than 5 minutes.)
   4. To re-run an analysis, click the analysis "App" in the 'Analyses' window.
7. Access analysis results in one of two ways:
   1. In the 'Analyses' window click on the analysis "Name" to open the output folder.
   2. In the 'Data' window, click on user name, then navigate to the folder that holds the output of the analysis. (Find the output for the sample at Community Data > iplant_training > rna-seq_without_genome > O_combine_counts > output_from_sample_data.)
8. The output table will have a common column for sequence names, and one individual column of counts for each sample or replicate. This file is ready to be analyzed with either DESeq or EdgeR.