Question: Help! RNA-seq validation options
gravatar for Paul Langdon
14 days ago by
Paul Langdon10
Paul Langdon10 wrote:

Hello all!

I would like to know if someone could guide me with the following: I am finalizing a transcriptomic analysis, however, due to the current health contingency I have not been able to access to the lab to validate the experiment by qPCR. Do any of you know of another way to validate this type of study or do you know of any journal that accepts this work without the need for qPCR validation? This situation for COVID-19 is getting longer and we do not see the moment when we can return to the lab, so we are looking for options to validate it or to publish without the need of using qPCR. I appreciate your responses in advance.

rna-seq next-gen • 73 views
ADD COMMENTlink written 14 days ago by Paul Langdon10

As a matter of fact I rarely see qPCR validation these days in papers (not saying this is good). It is probably luck if a reviewer demands it or not. Alternatively, maybe you can find published RNA-seq data similar to yours which you can analyze to increase confidence into your findings. Beyond that you could be quite stringent towards cutoffs, so test against a certain fold change (in DESeq2 that would be the lfc option of results and in edgeR the glmTreat function. Maybe something like log2(1.5) to be sure only the most reliable DEGs are retained.

In the end it all depends what your paper is about. If you make strong claims based on the RNA-seq and it is the basis for everything, then some validation is probably key. If it is one of many experiments, and you anyway have other data supporting your hypothesis then I'd probably not care too much about qPCR. All depends on the context. If the overall manuscript is excellent I do not think reviewers will bother you qith qPCR. If it is somewhat inconvincing then they might start asking for additional validation (rightfully so in this case).

ADD REPLYlink modified 13 days ago • written 14 days ago by ATpoint36k

Thank you very much for your answer!!

ADD REPLYlink written 13 days ago by Paul Langdon10
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