Import your reads

Use the appropriate Import button to import the reads in the Navigation Area of the Workbench.

Click on the folder icon (Image find_in_project_16_n_p) to the right of the "Select files" field, and select the files you want to import.

The Illumina High-Throughput Sequencing Import offers the following options (figure 13.2):

Image importguide
Figure 13.2: The Analyze QIAseq Samples Illumina Import dialog.

The Ion Torrent High-Throughput Sequencing Import (figure 13.3) just requires you to specify a SAM or BAM file containing unmapped reads.

Image importioguide
Figure 13.3: The Analyze QIAseq Samples Ion Torrent Import dialog.

Note that if your Ion Torrent reads are already mapped, they will be ignored by this importer, and a warning dialog will state that the SAM/BAM file contained more references than selected references, followed by a list of missing chromosomes and the number of reads aligning to these chromosomes. To import correctly mapped Ion Torrent reads, exit the Analyze QIAseq Samples guide and use the Import | Ion Torrent button in the Toolbar of the Workbench.