Build a set of index files for the Drosophila genome. An error message appears if you do not have the Bioinformatics Toolbox Interface for Bowtie Aligner support package installed when you run the function. Click the provided link to download the package from the Add-on menu.

For this example, the reference sequence Dmel_chr4.fa is already provided with the toolbox.

status = bowtie2build('Dmel_chr4.fa', 'Dmel_chr4_index');

If the index build is successful, the function returns 0 and creates the index files (*.bt2) in the current folder. The files have the prefix 'Dmel_chr4_index'.

Sometimes the index files exist, and you want to know the reference sequence used to build the index. In this case, use the bowtie2inspect function to get more information about the reference.

bowtie2inspect('Dmel_chr4', 'Dmel_chr4_retrieved.fa');

By default, the output file Dmel_chr4_retrieved.fa contains the sequence of the reference. You can also get a summary information about the reference name and lengths instead of the actual sequence. For details on the available options, see Bowtie2InspectOptions.

Once the index is ready, map the read sequences to the reference using the bowtie2 function. The paired-end read files (SRR6008575_10k_1.fq and SRR6008575_10k_2.fq) are already provided with the toolbox.

bowtie2('Dmel_chr4','SRR6008575_10k_1.fq','SRR6008575_10k_2.fq','SRR6008575_10k_chr4.sam');

The output is a SAM-formatted file that contains the mapping results.

You can specify different alignment options by passing in a Bowtie 2 syntax string or using a Bowtie2AlignOptions object.

Suppose you want to trim some residues from the 3' end before aligning. First, create a Bowtie2AlignOptions object.

 alignOpt = Bowtie2AlignOptions;

Trim four residues from the 3' end before aligning.

 alignOpt.Trim3 = 4;

Map reads to the reference using the specified alignment option.

flag = bowtie2('Dmel_chr4','SRR6008575_10k_1.fq','SRR6008575_10k_2.fq','SRR6008575_10k_chr4_trimmed.sam',alignOpt);