Hi, for syn22755055, is there a way to link libraryID to specimenID or individualID? It seems impossible to link the fastq files to individuals (and therefore phenotype) without such a mapping. Thanks!

Created by Gerald Quon geraldquon
We gave up, unfortunately, we couldn't figure out how to map.
Hi @geraldquon, we also have the same query about mapping the data to donors. Please could you share your strategy for this mapping. Thank you!
Got it. We also noticed that one of the fastq files was updated recently: d19-4298_s2_l004_r2_001.fastq.gz We actually were going to report that this file (that was replaced) seems to be corrupted. We also noticed another set of files corresponding to the following sample is similarly corrupted, but not updated: d19-4296*
Hi @geraldquon. Thanks for your question. The format of the metadata in this study deviates from our normal standards, so I understand the confusion. If you downloaded the files programmatically from syn22963646, you should have a manifest file accompanying your download that contains the libraryID to filename matching. The samples were hashed, so each fastq file has data from multiple individuals. The files were annotated with libraryID and that ID can be mapped to the assay metadata file (syn23583510) to identify the files that contain the hash tag oligos vs. 10x data. As I understand it from the data contributor, each fastq file will contain multiple barcodes. Those barcodes can be mapped to the donor identifier using the HTO-individualIDs mapping file (syn23583511). Then, donor-level metadata is available here - syn24226675. I'm a bit of a messenger here, having not analyzed this dataset myself, so if you run into further issues please let me know.
@kelab018 @cmolitor

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