Trim output

Clicking Next will allow you to specify the output of the trimming as shown in figure 21.14.

Image trimstep4
Figure 21.14: Specifying the trim output.

In most case, independently of what option are selected in this dialog, a list of trimmed reads will be generated:

However, if no sequences are trimmed using the parameter settings provided, then no sequence lists are output when running the tool directly. A warning message appears stating that no sequences were trimmed. When the tool is run within a workflow, and if no sequences are trimmed using the parameter settings provided, then all input sequences are passed to the next step of the analysis via the "Trimmed Sequences" output channel.

In addition the following can be output as well:

Image trimreport
Figure 21.15: 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.

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.