I was wondering whats the best way to extract the identifier of each differentially expressed gene? I've been told it's possible to compare it to a GFF file to obtain protein identifiers but I don't know how best to go about it. The output that I'm referring to is the output from the nbinomTest as performed on DEseq data, which has then been altered so only those with significant p values remain.
what are the identifiers in your counts table? For example, i make my counts table based on ensembl transcripts so i have an ENSMUST for each rowname.
This is an example of the identifer I'm using gi|222109225|ref|NC_011992.1|:c1488979-1488104 I'm a novice at this so I'm not quite sure what thats for