Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Can we extract full-length trascripts from gencode gtf

    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/G...otation.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
    Last edited by emanlee; 06-04-2014, 03:29 AM.

  • #2
    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!)
    Last edited by emanlee; 06-04-2014, 04:12 AM.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM
    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-28-2024, 06:12 AM
    0 responses
    27 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    74 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    82 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X