Generally when I receive RNA seq data, I get biological and technical replicates. IE if there are two conditions (eg treated vs untreated), there will be three samples Treated-A, Treated-B, Treated-C, each with two technical replicates, Treated-A-Lane1 and Treated-A-Lane2.
What most of my group has previously done is just run them all as individual replicates (i.e. n=6). The only thing I could see this benefiting is to average out technical variation between the samples.
The other way I could think to do it is just automatically combining the technical replicates to increase the sequencing depth.
What do you all do? Use the technical replicates separately to increase n / average more variation or combine them to increase the depth?
What most of my group has previously done is just run them all as individual replicates (i.e. n=6). The only thing I could see this benefiting is to average out technical variation between the samples.
The other way I could think to do it is just automatically combining the technical replicates to increase the sequencing depth.
What do you all do? Use the technical replicates separately to increase n / average more variation or combine them to increase the depth?
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