Mapping output options

Clicking Next lets you choose how the output of the mapping should be reported (see figure 30.10).

Image referenceassembly_step4
Figure 30.10: Mapping output options.

The main choice in output format is at the top of the dialog - the read mapping can either be stored as a track or as a stand-alone read mapping. Both options have distinct features and advantages:

Read more about both output types in Reads tracks and Stand-alone read mappings. Note that the choice you make here is not definitive: it is possible to convert stand-alone read mappings to tracks and tracks (reads and annotation tracks) to stand-alone read mappings (see Converting data to tracks and back).

In addition to the choice between the two main output options, there are two independent output options available that can be (de-)activated in both cases:

Finally, you can choose to save or open the results. Clicking Finish will start the mapping.