Extract sequences
This tool allows the extraction of sequences from other types of data in the Workbench, such as sequence lists or alignments. The data types you can extract sequences from are:
- Alignments (
)
- BLAST result (
) For BLAST results, the sequence hits are extracted but not the original query sequence or the consensus sequence.
- BLAST overview tables (
)
- sequence lists (
)
- Contigs and read mappings (
) For mappings, only the read sequences are extracted. Reference and consensus sequences are not extracted using this tool.
- Read mapping tables (
)
- Read mapping tracks (
)
- RNA-Seq mapping results (
)
Note that paired reads will be extracted in accordance with the read group settings, which is specified during the original import of the reads. If the orientation has since been changed (for example using the Element Info tab for the sequence list), the read group information will be modified and reads will be extracted as specified by the modified read group. The default read group orientation is forward-reverse.
Note! When the Extract Sequences tool is run via the Workbench toolbox on an entire file of one of the above types, all sequences are extracted from the data used as input. If only a subset of the sequences is desired, for example, the reads from just a small area of a mapping, or the sequences for only a few blast results, then a data set containing just this subsection or subset should be created and the Extract Sequences tool should be run on that. For extracting a subset of a mapping, please see Extract parts of a mapping.
The Extract Sequences tool can be launched via the Toolbox menu, by going to:
Toolbox | Classical Sequence Analysis (
) | General Sequence Analysis (
)| Extract Sequences (
)
First select the elements from which sequences should be extracted, and click Next. The following dialog (figure 15.1) allows you to choose whether the extracted sequences should be extracted as single sequences or placed in a new sequence list. For most data types, it will make most sense to choose to extract the sequences into a sequence list. But when working with a sequence list, where choosing to "extract to a new sequence list" would just create a copy of the same sequence list, choose to "extract to single sequences" to generate individual sequence objects for each sequence in the sequence list.
Figure 15.1: Choosing whether the extracted sequences should be placed in a new list or as single sequences.
Below these options, in the dialog, you can see the number of sequences that will be extracted. Click Next to choose where to save the output, and Finish to start the tool.