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.
- Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
- 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).
- Open the Join multiple tab-delimited files (Public Applications > Experimental > MaizeRNAseq > Join multiple tab-delimited files).
- Change 'Analysis Name' to Combine_Counts, add a 'Description' (optional), and use the default 'output folder'.
- Click on the Parameters tab.
- 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).
- Click on "Launch Analysis".
- Click on 'Analyses' from the DE workspace and monitor the 'Status' of the analysis (e.g., Idle, Submitted, Pending, Running, Completed, Failed).
- Once launched, an analysis will continue whether the user remains logged in or not.
- Email notifications update on the analysis progress; they can be switched off under 'Preferences'.
- 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.)
- To re-run an analysis, click the analysis "App" in the 'Analyses' window.
- Access analysis results in one of two ways:
- In the 'Analyses' window click on the analysis "Name" to open the output folder.
- 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.)
- 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.