Hi everyone, I am new to RNA-seq analysis and I'm trying to understand what to do with my data.
I have 60 biological samples (30 control and 30 diseased, paired samples). Each biological sample has 1 or two technical replicates. I will concatenate the .fastqc files for technical replicates to yield the biological replicate file. My issue is that biological replicates with only 1 technical replicate will have proportionally less reads than biological samples with 2 technical replicates. Is this correct? Is there anyway to overcome this? Is this an acceptable method?
Alternatively, I can work with the technical replicates and then average the reads for biological samples that have 2 technical replicates, so that proportionally biological replicates with 1 technical replicate are proportional to biological replicates with 2 technical replicates.
Either method (concatenating or averaging) when it comes to differential expression will compare relative expression values.
Reading the below Biostars discussion was useful: Technical replicates in RNAseq