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For your followup question @poojashukla about the predicted transcript identifiers (MSTRG), what to do next depends on what you have already done!
If you haven’t run a merge step yet (predicted along with known to “merge”), then you can do that. If the predicted transcripts overlap with a known transcript, the annotation will be merged and the known label applied.
Some features might not merge into a known gene bound. Those are your predicted novel features.
You can generate your final counts to use for DE against the merged version of the annotation (novel + known) or you can just use the known. Maybe do both and compare?
Similar topics have this same advice. Search results for 'stringtie mstrg' - Galaxy Community Help
This tutorial goes through the process. → Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics
Hope this helps! 