I have performed RNA-SEQ Data analysis using "HiSat2" -> StringTie -> Ballgown.... I used Ensemble Homo Sapiens Reference genome. The experiment contained Technical replicas and it was paired end.
I have done this analysis twice using two different pipelines, an old pipeline which contains Tophat2,Cufflinks,cuffmerge,Cuffdiff.... etc and a newer pipeline which is named "New Tuxedo package" as explained above.
In both cases, I had the DE list of genes, the problem is , some genes have no proper gene names, they have "." DOT in place of the name. My question is , How can i deal with these genes. What are they ?, i have many pseudogenes in the list and they have proper names, but some genes have no names at all only ".". How do you deal with this ?