Question: (Closed) Which step is better for merging technical replications?
0
gravatar for star
19 months ago by
star190
Netherlands
star190 wrote:

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?

ADD COMMENTlink modified 19 months ago by h.mon27k • written 19 months ago by star190
2

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!

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax72k

I am sorry, I agree with you!

Thanks!

ADD REPLYlink written 19 months ago by star190
1

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.

ADD REPLYlink modified 19 months ago • written 19 months ago by h.mon27k

Your answer is the one linked above :)

ADD REPLYlink written 19 months ago by genomax72k
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