Hi, I am looking to use the processed ROSMAP (snRNAseq - DLPFC, Experiment 2) data to compare AD and Control samples. It seems to me the data is currently separated into multiple files, each one sample. To do such comparison, would it be fine to merge all the files into one, and create a Seurat Object, or should I start from the raw data and run cellranger and cellranger aggr to merge them? Thanks! -Leo

Created by leo13692
Hello, Yes, you can merge all the processed files into one file to create a SeuratObject from it. However keep in mind that since these were run as separate samples, barcodes may be used in multiple files and you will need to do something like add a suffix to each barcode to indicate which file/sample it came from. For example, changing each barcode from `AAATTTCCCGGG-1` to `AAATTTCCCGGG-190403_B4_A` for files named "190403-B4-A". I recommend you change dashes to underscores like I did here, so Seurat knows that "-" is the separator between barcode and sample ID: (`CreateSeuratObject(..., names.delim = "-")`). An alternative would be to load each file as a separate SeuratObject and merge all the objects into one (see this tutorial https://satijalab.org/seurat/articles/merge_vignette.html), so Seurat handles the barcode renaming for you. Additionally, in case you weren't aware of this, you can use either [this file](https://www.synapse.org/#!Synapse:syn34572333) or [this file](https://www.synapse.org/#!Synapse:syn51218314) to map cell barcodes back to individual IDs. (I haven't checked, but the first file might have more barcode mappings than the second because I'm assuming the second includes some filtering of cells). I hope that helps! Let me know if you have any more questions about this. Jaclyn

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