Selecting reads and reference

To start the read mapping:

        Toolbox | NGS Core Tools (Image ngs_folder_open_16_n_p) | Map Reads to Reference (Image read_mapping_16_n_p)

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.

Image referenceassembly_step1
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.

Image referenceassembly_step2
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 (Image browse) 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 ( $ 2 \cdot 10^9$ bases) are not supported.