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CHAPTER 2. HIGH-THROUGHPUT SEQUENCING
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Figure 2.152: Specifying whether adapter trimming is needed.
Figure 2.153: Setting parameters for adapter trim.
It should be noted that if you expect to see part of adapters in your reads, you would typically
choose Discard when not found as the action. By doing this, only reads containing the adapter
sequence will be counted as small RNAs in the further analysis. If you have a data set where the
adapter may be there or not you would choose Remove adapter.
Note that all reads will be trimmed for ambiguity symbols such as N before the adapter trim.
Clicking Next allows you to specify additional options regarding trimming and counting as shown
in figure 2.154.
At the top you can choose to Trim bases by specifying a number of bases to be removed from
either the 3' or the 5' end of the reads. Below, you can specify the minimum and maximum
lengths of the small RNAs to be counted (this is the length after trimming). The minimum length
that can be set is 15 and the maximum is 55.