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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

RNA-Seq Analysis for Long Reads output

Output options are specified in the dialog shown in figure 8.4.

Figure 8.4: The output options for RNA-Seq using long reads.

The main results of the RNA-Seq analysis are Expression Tracks. A track with a name ending with (GE) summarizes expression at the gene level. If the "Genome annotated with genes and transcripts" option was selected, a second track, with a name ending in (TE), is produced, which summarizes expression at the transcript level.

In addition, the following outputs are available:

• Create reads track. This track contains the mapping of the reads to the references.
• Create report. A summary report.
• Create list of unmapped reads. This list is made of reads that did not map to the reference, or that were non-specific matches with more placements than specified.

Expression tracks

Expression tracks can be shown in a Table () and a Track () view.

The expression track table view has the following options (figure 8.5).

• The "Filter to selection" only displays pre-selected rows in the table.
• The "Create track from Selection" will create a new Track with the selected rows.
• The "Select Genes/Transcripts in Other Views" button finds and selects the currently selected genes or transcripts in all other open expression track table views.
• The "Copy Gene/Transcript Names to Clipboard" button copies the currently selected gene or transcript names to the clipboard.

Figure 8.5: A gene-level expression track shown in Table view.

For detailed information on expression tracks, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Expression_tracks.html.

RNA-Seq reads track

A track containing the mapped reads can be generated by the tool if the option to do so is enabled. The graphical view of the mapped reads can be shown together with the expression tracks in a Track list. For additional information on this output, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Expression_tracks.html.

RNA-Seq report

An example of first part of the RNA-Seq report is shown in figure 8.6.

For a detailed description of the different sections in the report, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_report.html.

Figure 8.1: Report of an RNA-Seq Analysis for Long Reads.

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