Editing a contig or read mapping
When editing contigs and read mappings, you are typically interested in confirming or changing single bases, and this can be done simply by:
selecting the base | typing the right base
Some users prefer to use lower-case letters in order to be able to see which bases were altered when they use the results later on. In CLC Genomics Workbench all changes are recorded in the history log (see History view), allowing the user to quickly reconstruct the actions performed in the editing session.
There are three shortcut keys for easily finding the positions where there are conflicts:
- Space bar: Finds the next conflict.
- "." (punctuation mark key): Finds the next conflict.
- "," (comma key): Finds the previous conflict.
In the contig or mapping view, you can use Zoom in (
) to zoom to
a greater level of detail than in other views (see figure 20.12). This is useful for discerning the
trace curves.
If you want to replace a residue with a gap, use the Delete key.
If you wish to edit a selection of more than one residue:
right-click the selection | Edit
Selection (
)
This will show a warning dialog, but you can choose never to see this dialog again by clicking the checkbox at the bottom of the dialog.
Note that for contigs or mappings with more than 1,000 reads, you can only do single-residue replacements (you can't delete or edit a selection). When the compactness is Packed, you cannot edit any of the reads.