Which GTF file to use while detecting known and novel non coding RNA
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Entering edit mode
6.9 years ago
mike ▴ 90

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

RNA-Seq GTF long non coding RNA • 1.9k views
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6.2 years ago

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.

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