How to combine RNA-Seq from Novaseq separated in lanes, after fpkm have been computed?

Question

[jamespower]

Hi,

I have been given two files with FPKM values computed on different lanes for the same sample, is it appropriate to sum the FPKM values by gene and sample across the different lanes?

Thank you for any help

Answer 1

[Michael]

I recommend to give the data back and ask for the raw data or at least raw counts. There is no proof that summing FPKM values is meaningful. Also FPKM should not be used as a unit for RNA-seq quantification. If the sequences are technical replication you can either merge the fastq files, the bam files after alignments (preferred, you are still able to detect differences in read quality or alignment rate) or sum the raw counts.