Extracting reads from mappings
This section describes functionality for extracting reads from stand-alone read mappings. Extracting reads from reads tracks and sequence tracks is described in Extracting sequences from tracks.
Reads can be extracted from stand-alone read mappings in multiple ways:
- Extract from Selection. Available from the right-click menu of the reference sequence or consensus sequence (figure 22.17). A new stand-alone read mapping consisting of just the reads that are completely covered by the selected region will be created. Options are available to specify the nature of the extracted reads (e.g. match specificity, paired status, etc.). These options are the same as those provided in the Extract Reads tool.
- Extract Reads. Available from the Toolbox. It extracts all reads or a subset of reads, specified based on location relative to a set of regions and/or based on specified characteristics of the reads. Reads can be extracted to a reads track or sequence list. See Extract Reads.
- Extract Sequences. Available from the right-click menu of the coverage graph or a read (figure 22.18), or from the Toolbox. It extracts all reads to a sequence list or individual sequences. See Extract sequences.
Figure 22.17: Right-click on the selected region on the reference sequence (left) or consensus sequence (right) in a stand-alone read mapping for revealing the available options.
Figure 22.18: Right-click on the coverage graph or reads for revealing the available options.