Can we extract full-length trascripts from gencode gtf

Question

[Aimin Li]

Hello, all

We can see that GENCODE released statistics and GTF annotation as follows:

(1) Statistics: (extracted gencode V19 from here)

• Protein-coding transcripts 81814
  • full length protein-coding: 57005
  • partial length protein-coding: 24809

(2) GTF file: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz

My question is how can we determine which transcripts are full-length or not?

Thanks a lot for your help in advance.

Aimin Li

Answer 1

[Aimin Li]

Sorry, I just got it:

• full length protein-coding -> the protein-coding transcripts that have no cds_start_NF or cds_end_NF tag
• partial length protein-coding: -> all the rest (they have either a cds_start_NF or cds_end_NF tag or both!)