Editing the read mapping

When editing 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 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:

In the mapping view, you can use Zoom in (Image zoom_in) to zoom to a greater level of detail than in other views (see figure 18.12). 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 (Image 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 mappings with more than 1000 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.