Hi,
Does anyone know how to normalize RNA-Seq data from subcellular fractions?
I have RNA-Seq data from the nucleus, insoluble, cytosolic, and membrane fractions, as well as from the whole cell.
The same amount of RNA was submitted for sequencing. Spike-in reads were included before ribosomal depletion.
Normalisation was performed relative to the spike-in reads.
In my opinion, the comparison between the fractions normalized relative to the spike-in reads is invalid since it does not take into account the different amounts of RNA in the fractions.
Any comments, opinions or advice on this issue?
Thank you.
Does anyone know how to normalize RNA-Seq data from subcellular fractions?
I have RNA-Seq data from the nucleus, insoluble, cytosolic, and membrane fractions, as well as from the whole cell.
The same amount of RNA was submitted for sequencing. Spike-in reads were included before ribosomal depletion.
Normalisation was performed relative to the spike-in reads.
In my opinion, the comparison between the fractions normalized relative to the spike-in reads is invalid since it does not take into account the different amounts of RNA in the fractions.
Any comments, opinions or advice on this issue?
Thank you.
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