Sequence trimming

Clicking Next will allow you to specify sequence trimming as shown in figure 28.13.

Image trimstep3a
Figure 28.13: Sequence trimming.

At the top, you can choose to Remove fixed number of bases by specifying a number of bases to be removed from either the 3' or the 5' end of the reads.

At least one of the options Remove on first read or Remove on second read (for paired reads) must be checked. If none are checked, reads are not trimmed.

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.