Remove Ligation Artifacts

During the adapter ligation step of the library preparation, it can happen that two different DNA sequences also get ligated together. These ligation artifacts are more prone to occur between short DNA fragments, such as the ones generated from FFPE samples. The tool Remove Ligation Artifacts removes reads which are likely the result of ligation artifacts. In addition, in cases of short fragments, a remnant of the common sequence can be found at the end of R1 reads. The tool will also remove these common sequence artifacts.

The tool can be found in the Toolbox here:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | Biomedical Utility Tools (Image utilities_closed_16_n_p) | Remove Ligation Artifacts (Image remove_ligation_artefact2_16_h_p)

In the first dialog (figure 6.8), select a read mapping (it can also be an rna-seq read mapping).

Image removeartifacts
Figure 6.8: Select a read mapping.

In looking for ligation artifact, for each read:

In looking for common sequence artifact, for single reads and broken pairs:

In looking for common sequence artifact for paired reads, the tool will trim the overhang of the read that extends further than the beginning of the paired read carrying the UMI.

The setting options for the Remove Ligation Artifacts tools are as follow (figure 6.9).

Image removeartifactsoptions
Figure 6.9: Set the parameters for the remove Ligation Artifacts tool.

Click Next to choose to Open or Save the tool output, i.e., the read mapping where the ligation and sequences artifacts have been removed. It is also possible to generate a read mapping containing the ligation artifacts, and a report.

This report can be used together with the Combine Reports tool (see