I processed and analyzed RNAseq data before. It was pretty straight forward with Star, featureCounts and edgeR.
I received a new dataset of 36 samples with SE sequence file. I expected 36 files with ~30 million reads. Instead, I got 108 files (18 samples/per lanes with ~ 10 million reads). 12 groups with 3 biological replicates.
It turned out, each sample was sequenced 3 times ( technical replicates). My understanding is that I do not need technical replicates for RNAseq only biological replicates.
When I asked why , the answer was :"This was safer way to do the analysis and reduce bias than analyzing each sample just 1 time 30 M reads. Raw count should be a sum of the lanes with the replicated samples: Lane 1, 2,3 and respectively Lane 4,5,6. The FastQ data should be looked at similarly as sum of the replicate lane values and this way the data still considered as 30 million reads per sample."
My question is that if this is the correct way to analyze it? To process all the 108 files, sum up the raw counts of the technical replicates and feed into edgeR as 36 samples in 4 experimental groups.
Your advice and help are highly appreciated.
Thanks a lot,