The question is regarding snRNA-seq data of the ROSMAP (465 individuals sequenced)
The mapping file syn34572333 contains cell barcodes for each libraryBatch and the corresponding individuals IDs. I filtered this file to contain only entries from libraryBatch 200225-B10-A
I also downloaded the processed files of the same libraryBatch 200225-B10-A from syn51121986 syn51121983 syn51121993 and I created a seurat object
Now the issue is that when I tried to check if all the barcodes from the counts/ seurat object are present in the mapping file, I found that they are not present, so I cannot know to whom the barcodes in the counts belong to.
The barcodes that intersect between mapping file cell barcodes column and serurat object/counts barcodes column are only 21654 and they diff in 47271 barcodes !! which makes finding the individuals IDs for the barcodes in the counts matrix impossible. (correct me if I am wrong please).
For example,
[1] "TCTGGCTGTTAGAAGT-1" "GGGCTACCAATATCCG-1" "CATTCCGAGTGCTACT-1" "CTTACCGGTGCTAGCC-1" "CCACCATTCCAGCCTT-1" "TAGGTACAGCCGTAAG-1"
are among the barcodes present in the processed file counts/seurat object from libraryBatch 200225-B10-A but are not available in libraryBatch 200225-B10-A in the mapping files, so I cannot trace which individuals they belong to.
I hope Dr @masashi can help. Thank you so much.
Created by Sherine Saber ssaber Hi Sherine,
Thank you for your question. Allow me to investigate this further and get back to you.
Best,
Victor
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