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Unfortunately, I just found out the libraries were prepped separately as well. Thanks for the advice!
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Well, dangit - I just heard back and the same sequencer was used but library prep was done separately. Bummer. Thanks for the assistance.
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Batch correction as you mention shouldn't even run, I expect ComBat-seq will yell at you about confounded covariates if you try.
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The actual experiment and collection of samples were done at same time. Library prep was definitely done by same person using same protocol…
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There should be no appreciable batch effect because of sequencing, as long as following is true. The same sequencer (or at least type i.e. …
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