Dear ResearchGate community,
I have a question regarding the possibility of a batch effect in my single-end bulk RNASeq data set: Some of my samples (10 out of 30) were sequenced 2x due to initial low read count (on two different days, same facility & instruments) and the reads were later concatenated prior to alignment. In your opinion, does this introduce a batch effect which ought to be accounted for?
Many thanks in advance.
Best,
Luise
Generally you want to treat all your samples the same way, as minor things can introduce bias (different person handling the samples, different batch of reagents, different flow cell etc). If you have any internal controls, use those for QC, if not, a housekeeping gene to check for possible biases on those 10 samples.
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