Creating a Trim adapter list based on the Trim Reads report

Since the automatic option works conservatively with data of low quality, you can benefit from creating a new Adapter Trim List based on the report generated by running the Trim Reads tool a first time.

  1. Start the Trim Reads tool.
  2. Select the reads you want to analyze (or a subset of these).
  3. Leave the Quality trimming settings as they are set by default.
  4. In the Adapter trimming step, make sure that the option "Automatic read-through adapter trimming" is selected and that no Adapter Trim List is specified.
  5. Leave the Sequence filtering settings at their default value, i.e. with no filtering.
  6. In the Result handling step ensure that "Create Report" is selected and click Finish.

Once the process is completed, open the report and scroll down to the last section named "5 Automatic adapter read-through trimming" (as seen in figure 22.9).

Image readthroughreport
Figure 22.9: Use the statistics of the read-through trimming to create a Trim adapter list.

To create a Trim adapter list with the read-though sequence from the report:

  1. In the report, copy the sequence of the detected "Read-through sequence". If the sequence is long, then copy only the first 19 to 24 bp.
  2. Go to New | Adapter Trim List.
  3. Click the Add row button.
  4. Type the name of the first adapter, for example Read 1 read-through adapter.
  5. Paste the copied sequence.
  6. Set the Reads option to First read.
  7. Choose the option Remove the adapter and the following sequence (3' trim).
  8. For reads without adapters choose the option Keep the Read.
  9. In the Set scoring dialog, leave the default settings and click Finish.
  10. Repeat for the procedure with the read-through sequence for read 2.
  11. Save the Trim adapter list before closing it.

You can now use this Trim adapter list in combination with the "Automatic read-through adapter trimming" option for optimal adapter trimming of all samples in your experiment.