Sequence filtering

Clicking Next will allow you to specify length trimming as shown in figure 25.13.

Image trimstep3
Figure 25.13: Trimming on length.

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.

You can also Trim reads to a fixed length of your choice, choosing whether to trim them starting from the 3' or the 5' end.

Finally you can choose to Discard reads below length. This can be used if you wish to simply discard reads because they are too short. Similarly, you can discard reads above a certain length. This will typically be useful when investigating e.g. small RNAs (note that this is an integral part of the small RNA analysis together with adapter trimming).