Hello, I am reaching out to get some insight on the details of QC that was performed after the libraries were sequenced. I couldn't find anything regarding UMI cutoff, ambient RNA, mRNA expression, doublets and etc. Since the barcodes, features, and matrix files for the libraries could only map to some of the demultiplexing file barcodes, I am assuming that QC was done. I would greatly appreciate any information regarding the specific QC procedures, thresholds, and software used, as well as whether low-quality nuclei, doublets, or ambient RNA contamination were identified and addressed. Understanding the preprocessing steps would help me avoid repeating analyses that have already been performed. Thank you very much for any insight on this. Mykhailo Zaporozhets

Created by Mykhailo Zaporozhets mishazap
Hello @wpoehlm, Thank you for pointing me in the right direction. I completely overlooked that information earlier. It provides all the details I needed regarding the QC process. I appreciate your time and assistance! Best regards, Misha
Hello @mishazap, Thanks for reaching out. I want to ask if you've seen the 'Single-nucleus RNA-seq analysis' part of the Synapse wiki here: https://www.synapse.org/Synapse:syn31512863. It looks like this part of the wiki might not have fully surfaced on the AD Knowledge portal study details page, so it may have been easy to miss. If this still doesn't provide the information you're looking for, I will tag the data contributors. Thanks! Will

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