I'm very new to scRNAseq analysis, and I really appreciate any inputs and comments. Your feedback would help me a lot.
I have been given 3 groups data (4 normal, 8 disease and 8 treatment samples), what is the workflow to identify how man cell types and also ID the cell types using reference dataset(http://mergeomics.research.idre.ucla.edu/PVDSingleCell/CellBrowser/?ds=PAHRatLungs#) in each group?
This question might sounds too general. Specifically, I wonder whether I need to merge data within each group and then perform analysis for each group separately? or I should merge and integrate all 20 samples together? For QC, from my limited understanding, I should perform QC on each samples (20 in total) before doing any computation analysis, right?
Thank you so much for the kindly help!
Yes, QC should be done on each sample individually. OSCA, the Bioconductor single-cell compendium https://bioconductor.org/books/release/OSCA/ is a great read. Spend some quality time going through it, it should cover 99% of what you need.
Thank you for the rely, appreciate it very much. I do have another question regarding to the tutorials. I noticed that there is another tool on scRNAseq, called "Seurat". I wonder which one is more easy to use, Seurat or Bioconductor? As far as I know they are similar on scRNAseq analysis.
I personally prefer Bioconductor over Seurat, but Seurat has a large userbase itself. The linked resource is outstandingly comprehensive with lots of background information on the "why's" in addition to the "how's", one major reason why I prefer it. Seurat is also fine though.
Thank you so much
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Cross-posted: https://bioinformatics.stackexchange.com/questions/15847/whats-the-difference-between-seurat-merge-and-integration