Hello,
In the SEA-AD assay metadata csv files, there's a column named "specimen suffix", which appears to be a concatenation of either the "specimenID" (in snRNA) or "libraryID" (in multiome) row value and a unique identifier. The very last number of these "specimen suffix" values appears to correspond to the prefix of file names throughout the SEA-AD datasets.
If the pattern above is true, there seems to be some inconsistencies in the assay metadata csv files:
In the multiome metadata csv, syn31141003, the order of the "libraryID" column values matches those in "specimen suffix".
In the snRNAseq metadata csv, syn31454453, the order of "specimenID" values DOES NOT match those in "specimen suffix". Is there an error mapping these Specimen IDs to Specimen Suffixices?
In the snATACseq metadata csv, syn31149113, there is no "specimen suffix" column. Is this deliberate or an error?
This question might be relevant to "Mapping hdf files to assay metadata" post, asked by @sumitisandhu so adding here.
Thanks,
Chris
Created by Chris Rhodes crhodes4 Thanks for clarifying @abby.vanderlinden ! Hi Chris,
The "specimen_suffix" column was provided by the data contributor and is a unique suffix for each library that allows translation between the barcodes in each fastq file with the cell names in each processed data file **(cell name = [barcode][specimen_suffix])**. I will add this information to the methods description on the SEA-AD study page.
"specimenID" and "libraryID" are standard columns that are part of our AD Portal data model. The specimenID refers to the physical biospecimen from which data was generated. In the multiome metadata, since two readouts are generated simultaneously from a single cell, the libraryID is used to indicate which snRNAseq and snATACseq data came from the same library preparation.
@eitan.kaplan or @timdol, can you confirm that the lack of a "specimen_suffix" column for the snATACseq metadata is deliberate, or an oversight? I can help make any changes if that is needed. Thanks!
Abby
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