the reference used in Cuffcompare(GENCODE, RefSeq)
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?
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I would doubt that. RefSeq is a curated database and if the transcript is present there it came from a reliable source.
Check AGAT toolkit. https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html
Thank you! I will check it out!