Note that this means that you cannot use a combination of paired-end and mate-pair data for batching.
Figure 8.4 shows the parameter dialog when running read mapping in batch.
Note that you can only specify one setting for all short reads, and one setting for all long reads. When the analysis is run, the reads are automatically categorized as either long or short, and the parameters specified in the dialog are applied. The same goes for all reads that are imported as paired where the minimum and maximum distances are applied.