I am interested in detecting known as well as novel long non coding RNA in mice RNA-Seq samples. While doing alignment I have used GTF with only Long non-coding RNA gene annotation (instead of using main annotation file with all annotations) from GENCODE. For the detecting novel long non coding RNA, I used RABT assembly from Cufflinks with out GTF file.
Can I skip using GTF while aligning?
If no, then which annotation file to be used? (subset with only Long non-coding RNA or main annotation file with all features)