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Example 3: Finding passenger genes

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mjsull edited this page Sep 15, 2015 · 1 revision

Example workflow for finding passenger genes of a transposon with long terminal repeats (LTRs) in a bacterial genome (Illumina)

  1. Create Contiguity-CAG using the command-line or GUI.

  2. Load CAG by selecting “Load Assembly” from the “File” menu.

  3. If the LTR contig has been identified select “Add contig” from “View menu”.

  4. Alternatively a multiFASTA of potential LTRs can be compiled and LTR contigs can be identified by generating a comparison to this file.

  5. Double click on transposon and select “Find paths” from the “Tools” menu.

  6. Check “Find all paths” and reduce “Max bp” to the maximum bases predicted for passenger genes.

  7. Select “Ok”.

  8. Arrange contigs (Duplicate LTR) and create scaffolds if needed.

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  1. Introduction to Contiguity
  2. Requirements
  3. Installation
  4. Citing Contiguity
  5. Workflow and Examples
  6. Finishing a PacBio HGAP assembly
  7. Ordering contigs
  8. Finding passenger genes
  9. Identifying plasmid contigs
  10. Menu overview
  11. File
  12. View
  13. Tools
  14. Viewing the Assembly
  15. Canvas overview
  16. Context menus
  17. Creating comparisons
  18. Comparison to a reference
  19. Self comparison
  20. Finding paths
  21. Creating scaffolds
  22. Creating scaffolds from a CAG
  23. Creating scaffolds from a PacBio Assembly
  24. Constructing a Contig adjacency graph
  25. CAG creation GUI
  26. CAG creation command-line

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