Opened 11 months ago

Last modified 11 months ago

#1558 closed enhancement

Add support for EPIC v2 — at Initial Version

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.51
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The EPIC methylation chip has come in a new version. The number of probes is different and there are several new probes and also many of the old ones that have been removed.

Our analysis depends on two files with metadata: EPIC.hg38.manifest.tsv and EPIC.hg38.mask.tsv. For the new chip version there are new files that should be used. We need to implement support for this in our pipeline so that it is possible to configure different metadata files (in reggie-config.xml) for different chips and to automatically select the correct files when creating the job script.

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