Pearson correlation between biological replicates
I have several libraries from RNA-seq. Two of them (which are biological replicates) have a Pearson correlation of 0.77. Can i consider them as replicates and continue wornking with them & how can I support the decision to work with them? otherwise it means i should repeat the experiment?
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Can you give some context? If these are like batch replicates from a cell line I would probably by concerned. If this is a cohort of patients using ex vivo material / biopsy samples, this might simply reflect the biological heterogeneity. A PCA plot (see e.g. the DESeq2 manual for example code on how to do that) is another useful diagnostic. Is anything strange with this respective sample like low sequencing depth?
they are replicates from the same plant cell line submitted to a certain treatment with modifications in the culture media. I carried out a fastQC analysis in order to remove low quality sequences and adapters, but i realized that this sample got more "dirty" after processing it.