N) Trim count tables

Owned by Branden Lau (Unlicensed)
Last updated: Apr 07, 2015Version comment
2 min read

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.

  1. Log into the Discovery Environment: https://de.iplantcollaborative.org/de/.
  2. Open the Cut Columns app (Public Applications > General Utilities > Text and Tabular Data > Cut columns).
    1. Change 'Analysis Name' to Trim_Count_Table_Control01, add a 'Description' (optional), and use the default 'output folder'.
  3. Click on the Input data tab.
    1. 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).
  4. Click on the Options tab.
    1. Under the 'Indicate the delimiter for the data file' field leave the delimiter set to 'Tab'.
    2. 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.
  5. Click on "Launch Analysis".
  6. 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.).
  7. 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.
  8. 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 > N_trim_count_tables > output_from_sample_data.)

Note: Rename the output files for the next section in order to differentiate them.

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