Hi, I am trying to match the cells in the count matrix to individuals using the barcodes. However, I found that the ROSMAP_snRNAseq_demultiplexed_ID_mapping.csv (syn34572333) does not cover all the barcodes present in the count matrix for the corresponding batch. For example, in the 190403-B4-A batch (syn51121931), there are 22,180 barcodes in the count matrix, but 4,124 of these barcodes cannot be found in the 190403-B4-A batch in the ROSMAP_snRNAseq_demultiplexed_ID_mapping.csv. This is quite strange. Could you please help? Thank you very much.

Created by zhijiehan103012
That's a good question. If you're looking for actual methods information, you will have to ask @masashi for that information. I did find where the sequencing center information is: [syn21073536](https://www.synapse.org/Synapse:syn21073536) contains scRNA-seq assay metadata, and has a `platformLocation` field which should say which sequencing center each sample was processed at. To map `specimenID` in this file to the `individualID` in the barcode mapping file, you will need [syn21323366](https://www.synapse.org/Synapse:syn21323366), which has both columns. I hope that helps!
Thank you, @jaclynbeck. I have another question. How do you handle technical duplicates from different sequencing centers (Broad and NYGC) when quantifying with CellRanger? I noticed that while batch information is included, the sequencing center (Broad vs. NYGC) is not specified in the counts matrix.
Hello, If I recall, the ID mapping file only contains barcodes for cells that could be confidently mapped to a single individual. Cells that were ambiguous, didn’t map, or failed some QC, might exist in the counts matrix but won’t exist in the ID file, so the extra cells can probably be discarded from the matrix. You may want to double-check with the contributor ( @masashi ) just in case though. I hope that helps! Jaclyn Beck

The barcode-individual pairing file does not include all barcodes in the count matrix. (ROSMAP, snRNAseq - DLPFC, Experiment 2, syn31512863) page is loading…