Trim count tables (app: Cut Columns)
Description: The Cut Columns app takes specified columns from a table and transfers them into a new table. Documentation: http://www.gnu.org/software/coreutils/manual/html_node/cut-invocation.html.
- Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
- Open the Cut Columns app (Public Applications > General Utilities > Text and Tabular Data > Cut columns).
- Change 'Analysis Name' to Trim_Count_Table_Control01, add a 'Description' (optional), and use the default 'output folder'.
- Click on the Input data tab.
- Select the 'Select a tabular text data file' field. Browse to the folder containing the idxstats output from the previous section (Count mapped reads) and input the file (Sample data: Community Data > iplant_training > rna-seq_without_genome > N_trim_count_tables > BAcon01.sorted.bam.idxstats.txt).
- Click on the Options tab.
- Under the 'Indicate the delimiter for the data file' field leave the delimiter set to 'Tab'.
- Under the 'Enter comma-separated list of columns to extract (ie. c1,c3)' field, enter c1,c3 for the comma-separated list of columns to extract.
- Click on "Launch Analysis".
- Repeat steps 2-5 for each idxstats file, adjusting the 'Analysis Name' to match (e.g. Trim_Count_Table_Control02, Trim_Count_Table_Dehyd01, etc.).
- 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 > N_trim_count_tables > output_from_sample_data.)
Note: Rename the output files for the next section in order to differentiate them.