Can I add the read counts to the re-sequenced read counts directly?

Question

[dz2353]

Hi there,

I have sequenced my samples twice. Can I add the first-time read counts to the second-time read counts directly? I just check the correlation and performed the PCA analysis. But I am not sure if I need to remove the batch effect?

Thanks for any answer and ideas.

Answer 1

[swbarnes2]

If you sequenced the exact same library twice, and used the same gene counting pipelines, yes, you can just combine them. Barring a qc problem, running the library over again doesn't add any technical error.