Which GTF file to use while detecting known and novel non coding RNA

Question

[mike]

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.

1. Can I skip using GTF while aligning?

2. If no, then which annotation file to be used? (subset with only Long non-coding RNA or main annotation file with all features)

Thanks

Answer 1

[azimzadeh.jam.sadegh]

If you use STAR Aligner for alignment, there is an option for two step alignment. First one is based on GTF file for known RNAs and the second finds novels.