the reference used in Cuffcompare(GENCODE, RefSeq)

Question

[ZZOYEA]

Hello. I am currently conducting RNA-seq analysis and trying to identify novel transcripts using Cuffcompare by comparing with a reference. I performed Cuffcompare using GENCODE annotation and found some novel transcripts. However, if a transcript already exists in RefSeq, can we still consider it novel? Is it classified as known?

I checked the novel transcripts in IGV, and I found that there was already information about those transcripts in RefSeq.

How can I resolve this issue when identifying novel transcripts? Is it possible to merge multiple annotation files for use?

[GenoMax]

However, if a transcript already exists in RefSeq, can we still consider it novel?

I would doubt that. RefSeq is a curated database and if the transcript is present there it came from a reliable source.

Is it possible to merge multiple annotation files for use?

Check AGAT toolkit. https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html

[ZZOYEA]

Thank you! I will check it out!