Changes between Version 4 and Version 5 of Ticket #1558


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Timestamp:
Dec 15, 2023, 8:51:47 AM (12 months ago)
Author:
Nicklas Nordborg
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  • Ticket #1558 – Description

    v4 v5  
    1 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.
     1The 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. Here is more information https://epicom.biomedcentral.com/articles/10.1186/s43682-023-00021-5
    22
    33Our 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.