RNAseq Genes Different By File

[nexgengirl]

Hi,

I have diff files from ~20 different RNA sequencing experiments. A common GTF file was utilized to make these diff files. The number and identity of the genes in the diff files is different in each file. Some genes overlap but some do not. My question is:

If a gene is not present in the diff file but was present in the GTF file does that mean it is not expressed?

Any clarification is greatly appreciated.

[dpryan]

It kind of depends on how the "diff files" were made. It could be that only significantly DE genes were written, or that these genes were just filtered out in some experiments, or something else entirely. Even if they were filtered out, I wouldn't necessarily take that to mean the genes aren't expressed, just that they didn't produce enough signal to be useful (assuming there was filtering done and, if so, done properly).