How to process batches to be able to correct for its effect

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3.3 years ago

paria ▴ 90

Hi everyone,

I'm working on the ALS patients and comparing cases and control of this disorder. I already did single nucleus RNA sequencing for my controls (which were randomized with the samples from different region of case and controls of the same patients and some controls). Now, I would like to do the single cell RNA seq for my controls. But I'm worried that for downstream analysis it could be complicated as for batch correction. I really appreciate if anybody has any experience like this or any recommendation. I have the option to process one of the cases with these samples once more. I was wondering if it worth to do so.

I appreciate any comments

batch-correction sample-randomization • 975 views

ADD COMMENT • link updated 3.3 years ago by rpolicastro 13k • written 3.3 years ago by paria ▴ 90

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Out of curiosity why are you performing both snRNA-seq and scRNA-seq on your control samples?

ADD REPLY • link 3.3 years ago by rpolicastro 13k

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Sorry, I meant sn-RNA sequencing by single cell. I did just sn-RNA seq.

ADD REPLY • link 3.3 years ago by paria ▴ 90

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Integration of datasets generally mitigates many of the effects of batch in standard single-cell analysis. See chapters 13 (and additionally 7) in OSCA, or the Seurat integration vignette.

ADD REPLY • link 3.3 years ago by rpolicastro 13k

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