• Manuals

Browse the manual

• Introduction to the Ab Initio Transcript Discovery Plug-in
• Large gap mapper
  • Overview
  • Parameters
• Transcript discovery
  • Algorithm and parameter description
  • Results
    • Annotations on the read mappings
    • Predicted genes table
    • Regions and events table
    • Summary report
    • Extract annotated reference sequences
  • Mitochondrion
• Installation
• Uninstall
• Bibliography

Mitochondrion

You will typically have very high coverage on the mitochondrion genome and this quickly becomes a problem for the transcript discovery. The high coverage means that there can often be millions of events that will take a very long time to analyze. For this reason, the transcript discovery will skip the reference sequences that have an average coverage higher than 1000.

For a standard human data set, this limit will target the mitochondrion genome specifically.

Please note that it is not recommended to exclude the mitochondrion genome as reference for the mapping since all the reads that map well on this reference sequence will try to find matches on other chromosomes. This will lead to false positive matches.

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