HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Read Mapping Global alignment setting resulting in too many unmapped reads (multiple tools)

3.8. Read Mapping Global alignment setting resulting in too many unmapped reads (multiple tools)

Who is affected

For all the below mentioned affected tools, this issue is relevant only if the parameter Global alignment has been selected. Note that this is not the default setting. Users will need to specifically have checked the Global alignment option for results to be affected by this issue.

 

What are the symptoms

  • The number of mapped reads is substantially lower that what is expected or what was seen with previous Workbench versions.
  • For paired read sets, the number of broken reads will be significantly higher than expected (as one of the mates will by mistake not be mapped).

What is affected

This issue affects users running the following tools in the following software:

'Map Reads to Reference', 'Map Reads to Contigs' and 'Add Reads to Contigs' (CLC Finishing Module) in:

  • CLC Genomics Workbench 7.5.3 through 8.0.2
  • CLC Cancer Research Workbench 1.5.4 through 2.0 / Biomedical Genomics Workbench 2.1 and 2.1.1
  • CLC Genomics Server 6.5.4 through 7.0.2

'RNA seq analysis' in:

  • CLC Genomics Workbench 8.0, 8.0.1 and 8.0.2
  • CLC Cancer Research Workbench 2.0 / Biomedical Genomics Workbench 2.1 and 2.1.1
  • CLC Genomics Server 7.0, 7.0.1 and 7.0.2

This issue was fixed in the following Workbenches and the corresponding Servers:

  • CLC Genomics Workbench 7.5.5, CLC Cancer Research Workbench 1.5.6 and CLC Genomics Server 6.5.6 - released August 18, 2015
  • CLC Genomics Workbench 8.0.3, Biomedical Genomics Workbench 2.1.2 and CLC Genomics Server 7.0.3 - released August 13, 2015

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