HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Error in bed format file output for non-continous annotations

3.7. Error in bed format file output for non-continous annotations

Who is affected

Users, who have exported annotation information to BED format from the below Workbench versions and where annotations consist of so-called block list entries (e.g.a mRNA made of of multiple exons).

Export of continuous annotations (e.g. genes of prokaryotes) are not affected.

  • CLC Genomics Workbench 8.5.1 and earlier
  • CLC Cancer Research Workbench 2.0 and earlier
  • Biomedical Genomics Workbench 2.5.1 and earlier
  • CLC Genomics Server 7.5.1 and earlier

What are the symptoms

The 12th column of the exported BED file, "blockStarts", according to the BED format should report the starting position of each 'block' of a feature (e.g. the individual exons) relatively to the start of the feature as reported in the "chromStart"column. The blockStarts column instead mistakenly gives the absolute genomics sequence coordinates for the start of exons.

Re-import of the BED file into the Workbench or import into alternate programs, will produce distorted annotation information.

When will this be fixed

This issue was fixed in the following versions, released in March, 2016:

  • CLC Genomics Workbench 9.0 
  • Biomedical Genomics Workbench 3.0
  • CLC Genomics Server 3.0

Knowledge Tags

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