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24 months ago
myfam128
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Do I need to merge bam files or collapse replicates? I am working on differential expression analysis and have 3 technical replicates for each sample from different library not lane. Is it recommended to merge bam files? The library sizes for example are 26801625 23261117 24614936 (counts )my question is that are the library sizes very different to be merged or collapse the read counts? will such estimate be true to the expression levels. How to move ahead any suggestions
You don't have to collapse the replicates for differential expression analysis. Having replicates is the best way to generate accurate and reliable results.
if they are true technical replicates you should consider merging them.
What is a "true" technical replicate: the same biological sample but for instance sequenced on a different lane.
Never, never (ever) merge biological samples because those are indeed the power you need to do sound DEG analysis.
I was not clear before . The starting material used was the same but different libraries were prepared and sequenced, so they must be technical replicates right?
Yes. I would inspect the samples separately on a PCA plot, and if they cluster close are basically identically (expected) then I would just merge them up.
Thanks for reply I will try PCA analysis