Trim output

Clicking Next will allow you to specify the output of the trimming as shown in figure 23.12.

Image trimstep4
Figure 23.12: Specifying the trim output.

No matter what is chosen here, the list of trimmed reads will always be produced. In addition the following can be output as well:

Image trimreport
Figure 23.13: A report with statistics on the trim results.

Click Next if you wish to adjust how to handle the results. If not, click Finish. This will start the trimming process. If you trim paired data, the result will be a bit special. In the case where one part of a paired read has been trimmed off completely, you no longer have a valid paired read in your sequence list. In order to use paired information when doing assembly and mapping, the Workbench therefore creates two separate sequence lists: one for the pairs that are intact, and one for the single reads where one part of the pair has been deleted. When running assembly and mapping, simply select both of these sequence lists as input, and the Workbench will automatically recognize that one has paired reads and the other has single reads.