To analyse MS-MLPA data, digested samples have to be linked to their undigested counterparts. This can be done manually for each sample in the comparative analysis tab (in the digested column). This is explained in more detail in section 6b of the Coffalyser.Net Reference Manual.
Coffalyser.Net also features automatic matching of digested and undigested samples. Automatic matching only works if the sample names are similar.
- After the fragment analysis, navigate to the comparative analysis tab.
- Right-click in the window and select Digested samples (For MS-MLPA) > Match Sample Automatically.
- Select the samples that you want to include in the comparative analysis.
- Click Start Comparative Analysis and click OK to continue.
If you are having difficulty with the automatic matching algorithm, try giving your samples the same name with the exception of a short identifier that indicates whether the sample was digested (e.g. 'DIG') or undigested (e.g. 'UN').
You can see the automatic matching of digested and undigested samples in action in the short video below.
In case you're unable to view the video on YouTube you can also watch it here.