Trim output

Clicking Next will allow you to specify the output of the trimming as shown in figure 18.14.

Image trimstep4
Figure 18.14: 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 18.15: A report with statistics on the trim results. Note that the Average length after trimming (232,8bp) is bigger than before trimming (228bp) because 2.000 very short reads were discarded in the trimming process.

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.