Question: Zero FPKM counts in a known coding gene
gravatar for Ricchio
3 months ago by
Rio de Janeiro
Ricchio0 wrote:

Hi, everyone

I am using eXpress to quantify gene expression by FPKM counts on a database with all genes of one Drosophila species

I would like to look at the expression of Y-linked genes in this species (that have only 1 copy in the entire genome) across many tissues. The point is that all genes were in principle correctly analysed, but two Y-linked genes that I known they are transcribed (by transcriptome assembly) show 0.00 as result in the FPKM count.

I have already checked for all possible troubles I could have made, but I don't understand why these strange results.

Also, the .BAM file that eXpress worked against the reference fasta was explored on the IGV and I saw the RNA-seq reads of these two Y chromosome genes.

Do you known what can be wrong in my data or in the eXpress software?

Thanks a lot for this support!!!

rna-seq alignment gene • 209 views
ADD COMMENTlink written 3 months ago by Ricchio0

Boa tarde Ricchio,

Are these genes very short / small, in terms of base-pair numbers? Quantifying abundance over such genes can be difficult. In addition, don't use eXpress; instead, use Kallisto, which was produced by the same group as eXpress but many years later.

Another good and 'modern' count abundance tool is featureCounts.

Finally, you will want to avoid FPKM normalisation - it's inefficient and produces unreliable statistical inferences.


ADD REPLYlink modified 3 months ago • written 3 months ago by Kevin Blighe21k
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