To start the read mapping:
Selecting reads and reference
Toolbox | NGS Core Tools () | Map Reads to Reference ()
In the first dialog, select the sequences or sequence lists containing the sequencing data (figure 24.1). Please note that reads longer than 100,000 bases are not supported.
Figure 24.1: Specifying the reads as input. You can also choose to work in batch.
When the sequences are selected, click Next, and you will see the dialog shown in figure 24.2.
Figure 24.2: Specifying the reference sequences and masking.
At the top you select one or more reference sequences by clicking the Browse and select element () button. You can select either single sequences, a list of sequences or a sequence track as reference. Note that single reference sequences longer than 2gb ( bases) are not supported.