Question: Can we extract full-length trascripts from gencode gtf
0
gravatar for Aimin Li
4.8 years ago by
Aimin Li30
Xi'an
Aimin Li30 wrote:

Hello, all

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

(1)  Statistics: (extracted gencode V19  from :  http://www.gencodegenes.org/stats.html  )

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

full-length gencode • 1.8k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Aimin Li30
3
gravatar for Aimin Li
4.8 years ago by
Aimin Li30
Xi'an
Aimin Li30 wrote:

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!)

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Aimin Li30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1163 users visited in the last hour