Hi,
I aimed to detect novel transcript with HIFI reads using stringtie2(guided mode). Then I compare the result to gencode(v44) annotation. But almost half of the novel transcripts are marked as "s". Should I discard these kind of transcripts? And which class codes could be considered as novel transcripts expect class code "u"? And I aligned the reads to GRCh38 with minimap2(newest version, recommend parameter). Thanks!
Hi, I aimed to detect novel transcript with HIFI reads using stringtie2(guided mode). Then I compare the result to gencode(v44) annotation. But almost half of the novel transcripts are marked as "s". Should I discard these kind of transcripts? And which class codes could be considered as novel transcripts expect class code "u"? And I aligned the reads to GRCh38 with minimap2(newest version, recommend parameter). Thanks!