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Raw data files present in the study must have file format annotated as “fastq” or “bam” or “cram”
If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.
Data files must originate from samples that were “flash frozen”. Data from FFPE samples are not eligible for processing due to possible degradation of genomic samples due to the preservation process.
Data files must have the required minimal annotations according to the NF-OSI data model (as suggested in the NF Data Curator App). These annotations include among others:
individualID
specimenID
assay
libraryPreparationMethod
Platform
isStranded
readPairOrientation
readPair
specimenPreparationMethod
isCellLine
isXenograft
Only raw data files uploaded to Synapse projects are eligible to be staged for processing at this time.
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