How is it possible to have more than 25000 genes in counts file?

Question

[Batu]

Hello everyone,

I have a question about RNA-seq for Homo sapiens. Humans have about 25000 genes which are protein-coding. But in my recent analysis, there are more than 58000 genes with their Ensembl Gene IDs inside my counts file. How is it possible? Did I miss something while processing the fastq's and it caused an error? Thanks...

Answer 1

[Devon Ryan]

Not all genes are protein coding.

[i.sudbery]

and 58,000 is about right for the full gene set including non-coding.

[Emily]

Current counts

Answer 2

[Friederike]

How is it possible to have more than 25000 genes in counts file.

If your annotation file (most likely a GTF file?) that you used for generating the counts contained more than 25K gene IDs.

For more details than you might ever want to know about annotation caveats, I recommend reading "A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification."