NGS_DNA
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FAQ

Demultiplexing

Pipeline stopped in first step (Bcl2FastQ).

Cause: The samplesheet is corrupt
Solution:
    check if there are no windows signs in the samplesheet (^M) → mac2unix
    No empty lines at the bottom (NB: empty means only comma’s)
    Are there required fields written with ‘none’ instead of ‘None’

All the reads are discarded

Possible cause: There is an unknown barcodeType, the step will crash.
Solution: Fill in a barcodeType in the samplesheet that is valid (and create an issue in molgenis-pipelines on github that a new barcode should be added to the known barcodeTypes

Pipeline is not producing correct data

Possible cause: Are there dual barcodes?
Solution: In case of dual barcodes, the second barcode should be reversed complement

NGS_DNA