How to differentiate between two biological replicates

Question

[ancient_learner]

Hi I need to analyze the replicates generated through paired-end sequencing, individually, to show the consistency between the replicates. I have pooled the replicates when I was doing the analysis initially. Now If I want to start from the alignment results (.bam format) rather from .fastq files how should I differentiate between two replicates? I see for both of them the read Ids are similar since they were run on same machine at the same time. Is there any way for this?

[ancient_learner]

Just now noticed that the adapter is different so think I can manage with that

[Benn]

If you want to see the 'consistency' between two samples, you might want to try how they correlate. Calculate the Pearson correlation between your samples, and ideally also calculate the correlation between samples that are not replicates (to see the difference).

So align your fastq files, separately, to your genome of interest, and get raw read counts from you bam files with featureCounts (or some similar software). Use these counts for correlation.

Another way is to use the MDS plot in edgeR (if you also have more non-replicate samples).