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?
This was already answered: C: Merging RNA-seq sample with several replicate in which step?
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I am sorry, I agree with you!
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.
Your answer is the one linked above :)