Basic and nieve Question in lncRNA analysis pipeline

[rajeev.vikram]

Hi,

I have been analyzing RNA-Seq data sets of some Breast cancer cell lines to create a high confidence list of expressed lncRNAs. However as, I am new to NGS, I cannot figure out how do I filter out the known Expressed gene/protein coding transcripts from my annotation file after cufflinks assembly? Are there any specific tools to do the filtering? If anyone could help me regarding this, I will really appreciate.

Thanks