HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Annotation tracks of some large genomes affected in GWB 6.0.3 and earlier

3.22. Annotation tracks of some large genomes affected in GWB 6.0.3 and earlier

Summary description

An important issue has come to our attention associated with the annotation of genome tracks for organisms other than human, where

  • there are more than 22 autosomes and
  • where the annotation files used contain references to an X chromosome and/or a Y chromosome and/or a mitochondrial sequence.  

This issue only affects annotations imported as tracks or those annotations that have been applied via Download Genomes.

For the genomes available via the Download Genome functionality of the Genomics Workbench 6.0.3 and earlier, this affects:

Bos taurus: where incorrect annotations were applied to chromosome 23 and 25, and no annotations are placed on the X chromosome and the mitochondrial reference

Danio rerio: where incorrect annotations were applied to chromosome 25 and no annotations were applied to the mitochondrial reference.

Gallus gallus: where incorrect annotations were applied to chromosome 25 and no annotations were applied to the mitochondrial reference.

 

Recommended action if your data may be affected

We highly recommend that anyone working with data for these organisms, or those how have applied track-based annotations for any other organism matching the description given in the first paragraph:

 

Further details

The identified issue causes the following general problems when importing a track from an annotation file:

  • Annotations in the file for the X chromosome (see synonyms affected in the table below) will have been applied to a chromosome called chr23, 23 or chromsome_23, and no annotations will have been applied to the X chromosome itself.
  • Annotations in the file for the Y chromosome (see synonyms affected in the table below) will have been applied to a chromosome called chr24, 24 or chromsome_24 and no annotations will have been applied to the Y chromosome itself.
  • Annotations in the file for the mitochondria (see synonyms affected in the table below) appearing on a chromosome called chr25, 25 or chromsome_25 and no annotations will have been applied to the mitochondrial reference itself.

Several synonyms would be recognized for each of the sequences mentioned above in annotations files. If the labels being used in your annotation files do not match any of these, then your data will not be affected by this issue.

 

Reference Sequence names and synonyms
chromosome X X, chrX, chromosome_X
chromosome Y Y, chrY, chromosome_Y
mitochondria M, MT, chrM, chrMT, chromosome_M, chromosome_MT
chromosome 23 23, chr23, chromosome_23
chromosome 24 24, chr24, chromosome_24
chromosome 25 25, chr25, chromosome_25

 

 

This issue does not affect:

  • any organism where the genomic data or the annotation files do not have greater than 22 autosomes
  • any organism where the annotation file did not refer to an X chromsome, a Y chromsome or a mitochondrial sequence
  • any annotations applied to sequence objects or sequence lists using the Annotate with GFF tool
  • any annotated sequences imported as sequence objects or sequence lists directly, or downloaded using the Search at NCBI functionality
  • any track-base annotations generated using Convert to Tracks after importing  sequence objects or sequence lists directly, or downloaded using the Search at NCBI functionality
  • any organism where the naming scheme for the annotations for the X, Y or mitochondrial reference had names that are not in the synonym list provided above.

The current RNA-seq tool makes use of reference data in sequence objects or sequence lists objects, not tracks. If your references were not generated from tracks,  then your data, and thus results, are not affected by this issue.

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