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• Introduction
  • The concept of Long Read Support
  • Contact information
  • System requirements
• Template workflows
  • De Novo Assemble Long Reads and Polish with Short Reads
• Import Nanopore Reads
• De Novo Assemble Long Reads
  • De novo assembly parameters
  • De novo assembly output
• Map Long Reads to Reference
  • Map Long Reads to Reference output
• Polish with Reads
  • Polish with Reads output
• Correct Long Reads
  • Correct Long Reads output
• RNA-Seq Analysis for Long Reads
  • Reads and reference settings
  • Mapping settings
  • Expression settings
  • RNA-Seq Analysis for Long Reads output
• Structural Variant Caller for Long Reads
  • Structural Variant Caller settings
  • Structural Variant Caller output
  • Structural Variant Caller algorithm
• Install and uninstall plugins
  • Installation of plugins
  • Uninstalling plugins
• Bibliography

Mapping settings

In the next dialog, set the mapping parameters (figure 8.2).

Figure 8.2: Define mapping settings for RNA-Seq Analysis for Long Reads.

The generic mapping parameters are identical to those applied for Map Long Reads to Reference, see Map Long Reads to Reference.

In addition, the following RNA-Seq specific setting is available:

• Maximum number of hits for a read. Reads mapping equally well to more places than this number will be ignored. If a read matches to multiple distinct places, but less than or equal to the specified maximum number, it will be assigned to one of these places by the EM algorithm.

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