Question: How to combine RNA-Seq from Novaseq separated in lanes, after fpkm have been computed?
0
gravatar for jamespower
12 months ago by
jamespower40
jamespower40 wrote:

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

rna-seq next-gen gene • 293 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by jamespower40
6
gravatar for Dr. Mabuse
12 months ago by
Dr. Mabuse47k
Bergen, Norway
Dr. Mabuse47k wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Dr. Mabuse47k
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