Interpreting an FPKM of 0

[mmcgo002]

I am still unclear of how to interpret an FPKM of 0 which you get for some genes in the cufflinks outputs.

Does this mean that no reads have been mapped to this gene and therefore this gene can be considered as not a part of the transcriptome?

Or does this mean that the gene is expressed but it is below a certain threshold, and if so should they be excluded from future analyses or comparisons.

I am not doing a differential expression analysis--I'm just interested in what genes are or are not expressed, as I am doing a multi-species comparison between various mammalian species with genome assemblies.

[Wallysb01]

If you actually go look at a few genes with an FPKM of 0 on something like IGV, you'll see that sometime there are a few reads that align to it. Its just that when you're talking about 100M or more reads per sample, 1 or 2 reads is pretty insignificant. So, while you can't really say its not expressed with 100% certainty, you can say it was not detected. The other measure you can look at is if the low of the 95% confidence interval is >0. Then you can confidently claim something is expressed.

[cw11]

Side note - which version are you using? (I ask because there were some problems with 1.1.0 listing FPKMs as 0 when there were actually reads that mapped to those genes). I think they fixed this problem in 1.2.0.

[mmcgo002]

Thanks--that clears up that issue! I was using 1.1.0 but now I'm using 1.2.0. I think I'll rerun everything in 1.2.0, thanks for the heads-up!