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alevar / chess3_construction

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How did you define novel? #2

Open dudududu12138 opened 1 week ago

dudududu12138 commented 1 week ago

Hi, After assemble with stringtie, how did you define novel transcripts that not in gencode or refseq database? Just by the matching of intron chain? Did you treat a transcript as novel if the class code of it is not "=" ? Thanks! Looking forward to your reply.

alevar commented 6 days ago

Hi,

Yes, throughout the construction of the catalogue the intron chain compatibility ("=" code produced by gffcompare) was used to separate known from novel transcripts (with exception of single-exon transcripts which were processed separately and their novelty assignment might not be as reliable due to the differences at the 3' and 5' ends). In the final catalogue, this information is stored under the "db_xref" tag. If a transcript had assembly_id assigned and no db_xref tag, then it was treated as novel.

Hope this helps,

Ales