When you select the Tools ‣ Align to reference ‣ Align short reads item in the main menu, the Align Short Sequencing Reads dialog appears. Set value of the Align short reads method parameter to Bowtie 2. The dialog looks as follows:
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You can also configure other parameters. They are the same as in the original Bowtie 2 (you can read detailed description of the parameters on the Bowtie manual page).
Select one of the following alignment modes:
The -n alignment The --end-to-end alignment mode:
When the -n mode is selected, Bowtie determines which alignments are valid according to the following policy. Alignments may have no more than N mismatches (where N is a number 0-3) in the first L bases (where L is a number 5 or greater, set with Seed length) on the high-quality (left) end of the read. The sum of the Phred quality values at all mismatched positions (not just in the seed) may not exceed E (set with Maq error). Where qualities are unavailable (e.g. if the reads are from a FASTA file), the Phred quality defaults to 40.
The -v alignment mode:
In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3. Quality values are ignored. The -v mode is mutually exclusive with the -n mode.
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