[ensembl-dev] Rat codelink alignment and transcript annotations

Nathan Johnson njohnson at ebi.ac.uk
Mon Jul 11 14:38:00 BST 2011


An issue has been identified with the alignments and transcript annotation for the rat codelink array.

During the array import and mapping process for the rat Codelink array, a fasta file was erroneously truncated.  This did not affect the import of the array design (i.e. probes), hence passed our current health checks.  However, it did impact on the genomic and transcript alignment steps, resulting in only 30% of the probes being aligned to the genome rather than ~90%. In turn this impacted on the transcript annotation step which assigned xrefs to only ~15% rather than ~50% of the Codelink probes.  A new health check will be added to the array mapping pipeline to prevent this in future. Updated MySQL dumps are available here
	
	ftp://ftp.ensembl.org/pub/misc/codelink_fix_rattus_norvegicus_funcgen_63_34.tar.gz

This affects Ensembl releases up to and including version 63.


Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

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