Separate transcripts by type (app: Numeric Evaluation of a Data Column)
Description: This App identifies rows in a tab-delimited file where a specified column has a value that fits a specific criterion. Used to make separate lists of transcripts that have a fold-change value greater than or less than 1. Documentation: https://pods.iplantcollaborative.org/wiki/display/DEapps/Numeric%20Evaluation%20of%20a%20Data%20Column.
- Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
- Open the Numeric Evaluation of a Data Column app (Public Applications > General Utilities > Text and Tabular Data > Numeric Evaluation of a Data Column).
- Change 'Analysis Name' to Collect_Up-regulated_Transcripts, add a 'Description' (optional), and use the default 'output folder'.
- Click on the Select input data tab.
- Under the 'Select an input file' field enter the DESeq_results_significant.txt file from the previous section (Determine differential expression) (Sample data: Community Data > iplant_training > rna-seq_without_genome > Q_separate_transcripts_by_type).
- Click on the Options tab.
- Select the 'Indicate the test column (c1 = column 1)' field. Set the column to c6.
- Select the 'Enter either another column or a number' field. Enter 1.
- Select the 'Select a comparison operator' field. Choose "Greater than".
- Under the 'Lines of header text' field. Enter 1.
- Click on "Launch Analysis".
- Repeat steps 3-8, but set the comparison operator to “Less than” to determine which transcripts were down-regulated, changing the 'Analysis Name' to Collect_Down-regulated_Transcripts.
- 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 > Q_separate_transcripts_by_type > output_from_sample_data.)
- The output file, numeric_filter_out.txt, will be similar to DESeq_results_significant.txt from the previous section (Determine differential expression), but include only the lines corresponding to transcripts that DESeq determined were significantly up-regulated or down-regulated.
Note: Rename the output files for the next section in order to differentiate them.