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Which step is better for merging technical replications?

I have 3 technical replicates, and I have .fastq file (Raw data), .bam file (after alignment) and count table file for each of them. I would like to merge them together, which step is better to merge them?

rna-seq genome alignment sequencing
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updated by h.mon h.mon • written by star star

Hello star!

This was already answered: C: Merging RNA-seq sample with several replicate in which step?

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by GenoMax GenoMax

I am sorry, I agree with you!

Thanks!

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written by star star

I personally prefer to combine counts, after inspecting for possible batch effects. Also, if you already have all three, it is the fastest to merge. DESeq2 has the collapseReplicates() function for combining technical replicates counts.

edit: sorry genomax, the post was open on my browser and I didn't see you (correctly) closed the question.

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written by h.mon h.mon

Your answer is the one linked above :)

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written by GenoMax GenoMax

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