Dears,

When I did RNA-Seq and ChIP-Seq downstream analysis with GENE annotation of ENSEMBL. The final results are flooded with genes such as Gm's and Rik's.
[Based on Ensembl 'biotype' classifications in mouse, genes starting with 'Gm-' or ending with 'Rik' include protein-coding RNAs, long non-coding RNAs, and antisense transcripts.][1] 


  [1]: https://biostar.usegalaxy.org/p/18635/

Is it a proper way to filter out these genes before downstream analysis?


You could just use a RegEx if you're really keen to filter them. But they're real genes - we just don't know much about them yet.