• Product manuals

Browse the manual

• Introduction
• Large Gap Read Mapping
• Transcript Discovery
  • Running the Transcript Discovery tool
  • Transcript Discovery output
    • Tracks
    • Gene table
    • Summary report
    • Export and compatibility
  • The Transcript Discovery algorithm
• Install and uninstall plugins
  • Installation of plugins
  • Uninstalling plugins
• Bibliography

Gene table

This table contains a row for each predicted gene. If annotation tracks were specified during the tool set up, annotations marked with a * in the following list are included in the table.

• Reference. The name of the chromosome or mapping in which the gene was predicted.
• Gene. The name of the gene if it was annotated prior to the analysis. If it is a new predicted gene the name will be 'Gene' followed by a number (e.g. 'Gene_1').
• Unknown*. No if the gene was annotated prior to the analysis; yes if it is a new predicted gene.
• Length. The length of the gene region.
• Start. The start of the gene region.
• End. The end of the gene region.
• Strand. The strand on which the gene was predicted.
• Transcripts. The number of detected transcripts for the gene (including prior annotated as well as new predicted).
• Known transcripts*. The number of prior annotated transcripts for the gene that were detected as being expressed in the sample.
• Unknown transcripts*. The number of new predicted transcripts for the gene.
• Longest transcripts. The length of the longest transcript for the gene.
• Novel splice junctions*. The number of novel splice junctions.
• Reads. The sum of the read counts of the events from which the transcript annotations were built.
• Spliced reads. The sum of the spliced read counts of the events from which the transcript annotations were built.
• New 5' sequence*. Yes, if the gene region extends 5' of the prior gene annotation if there was one, else no.
• New 3' sequence*. Yes, if the gene region extends 3' of the prior gene annotation if there was one, else no.
• Splicing description*. A summary of the types of new splice sites found for transcripts for the gene ('Alternative acceptor/donor' and/or 'new exon').

Note, that while predicting genes and CDS's, the Transcript Discovery tool will also attempt to identify the strandedness. The strandedness is determined from the canonical splice sites in the spliced reads. However, sometimes that information is not present for some of the predicted genes. This can be because there are no spliced reads or because those that are there do not use any of the canonical splice sites. In these instances, the strand will be indicated with a "?" because it can not be determined.

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