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Transcript Discovery


Relying heavily on reads mapped with a gap as evidence for transcripts, the plugin is primarily developed for eukaryotic genomes. The proposed workflow for using the ab initio Transcript Discovery plugin in combination with the existing RNA-seq tool in CLC Genomics Workbench is this:

  • Run the large gap mapper using all your RNA-seq reads and a genomic reference sequence
  • Run the transcript discovery algorithm on the resulting read mapping to predict transcripts and genes
  • Inspect the results and if necessary re-run the transcript discovery to refine the settings to produce the desired result
  • Part of the result from the transcript discovery is a copy of the reference genome including the new transcript and gene annotations
  • This can now be used as a common reference for measuring gene expression using the existing RNA-seq tool in the workbench

If you have sequenced several samples that need to be compared, we suggest using the reads from all samples for the large gap mapping and subsequent transcript discovery. This way, you can establish a common set of reference transcripts and genes that makes it possible to compare gene expression levels across samples (using the RNA-seq tool in CLC Genomics Workbench). The initial read mapping created by the large gap mapper is then no longer used and can be deleted, unless you wish to be able to go back and double-check the basis of the prediction.

Check out the blog featuring this plugin

We frequently release updates and improvements such as bug fixes or new features. To get a complete overview, please visit the Latest Improvements page.

Downloads

Plugin Manual
Online manual Download manual
Plugin Download
Download plugin
Download Transcript Discovery (Beta)

Version

Platform support

Download

20.0.0

QIAGEN CLC Genomics Workbench


 [20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

3.0.0

QIAGEN CLC Genomics Workbench


 [12.0.4, 12.0.3, 12.0.2, 12.0.1, 12.0]

2.1.0 Beta v.1

QIAGEN CLC Genomics Workbench


 [11.0.2, 11.0.1, 11.0.0]

2.0.0 Beta v.17

QIAGEN CLC Genomics Workbench


 [10.1.3, 10.1.2, 10.1.1, 10.1.0, 10.0.1, 10.0]

2.0.0 Beta v.16

QIAGEN CLC Genomics Workbench


 [9.5.4, 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1, 9.0]

2.0 Beta v.14

QIAGEN CLC Genomics Workbench


 [8.5.4, 8.5.3, 8.5.2, 8.5.1, 8.5, 8.0.3, 8.0.2, 8.0.1, 8.0]

2.0 Beta v.13

QIAGEN CLC Genomics Workbench


 [7.5.5, 7.5.4, 7.5.3, 7.5.2, 7.5.1, 7.5]

2.0 Beta v.12

QIAGEN CLC Genomics Workbench


 [7.0.4, 7.0.3, 7.0.2, 7.0.1, 7.0]

2.0 Beta v.11

QIAGEN CLC Genomics Workbench


 [6.5.2, 6.5.1, 6.5]
Server Plugin Download
Download plugin
Download Transcript Discovery Server Plugin (Beta)

Version

Platform support

Download

20.0.0

QIAGEN CLC Genomics Server


 [20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

3.0.0

QIAGEN CLC Genomics Server


 [11.0.4, 11.0.3, 11.0.2, 11.0.1, 11.0]

2.1.0 Beta v.1

Biomedical Genomics Server Solution


 [10.0.2, 10.0.1, 10.0]

QIAGEN CLC Genomics Server


 [10.0.2, 10.0.1, 10.0.0]

2.0.0 Beta v.17

Biomedical Genomics Server Solution


 [9.1.3, 9.1.2, 9.1.1, 9.1, 9.0]

QIAGEN CLC Genomics Server


 [9.1.3, 9.1.2, 9.1.1, 9.1.0, 9.0]

2.0.0 Beta v.16

Biomedical Genomics Server Solution


 [8.5.4, 8.5.3, 8.5.2, 8.5.1, 8.5, 8.0.1, 8.0]

QIAGEN CLC Genomics Server


 [8.5.4, 8.5.3, 8.5.2, 8.5.1, 8.5, 8.0.1, 8.0]

2.0 Beta v.14

Biomedical Genomics Server Solution


 [7.5.4, 7.5.3, 7.5.2, 7.5.1, 7.5, 7.0.3, 7.0.2, 7.0.1, 7.0]

QIAGEN CLC Genomics Server


 [7.5.4, 7.5.3, 7.5.2, 7.5.1, 7.5, 7.0.3, 7.0.2, 7.0.1, 7.0]

2.0 Beta v.13

Biomedical Genomics Server Solution


 [6.5.6, 6.5.5, 6.5.4, 6.5.3, 6.5.2, 6.5.1, 6.5]

QIAGEN CLC Genomics Server


 [6.5.6, 6.5.5, 6.5.4, 6.5.3, 6.5.2, 6.5.1]

2.0 Beta v.12

Biomedical Genomics Server Solution


 [6.0.5, 6.0.4, 6.0.3, 6.0.2, 6.0]

QIAGEN CLC Genomics Server


 [6.0.5, 6.0.4, 6.0.3, 6.0.2, 6.0]

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