Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • Minseok Seo
    Junior Member
    • Oct 2014
    • 1

    #1

    gff > gtf transformation problem

    I want to generate gtf file for RNA-seq analyse...

    But, I experienced my first for performing RNA-seq analysis without gtf file.

    Input data are as following :

    Chr0 GLEAN mRNA 13595835 13596290 0.919626 + . ID=Cla000001;
    Chr0 GLEAN CDS 13595835 13596290 . + 0 Parent=Cla000001;
    Chr0 GLEAN mRNA 22577757 22577987 0.831796 + . ID=Cla000002;
    Chr0 GLEAN CDS 22577757 22577987 . + 0 Parent=Cla000002;
    Chr0 GLEAN mRNA 258813 259526 0.919626 + . ID=Cla000003;
    Chr0 GLEAN CDS 258813 259526 . + 0 Parent=Cla000003;
    Chr0 GLEAN mRNA 301272 301643 0.867498 - . ID=Cla000004;
    Chr0 GLEAN CDS 301272 301643 . - 0 Parent=Cla000004;
    Chr0 GLEAN mRNA 319902 320398 1 - . ID=Cla000005;
    Chr0 GLEAN CDS 320342 320398 . - 0 Parent=Cla000005;
    Chr0 GLEAN CDS 319902 320039 . - 0 Parent=Cla000005;
    Chr0 GLEAN mRNA 6029352 6029806 1 + . ID=Cla000006;
    Chr0 GLEAN CDS 6029352 6029441 . + 0 Parent=Cla000006;
    Chr0 GLEAN CDS 6029549 6029806 . + 0 Parent=Cla000006;
    Chr0 GLEAN mRNA 393272 393487 0.999939 + . ID=Cla000007;
    Chr0 GLEAN CDS 393272 393487 . + 0 Parent=Cla000007;
    Chr0 GLEAN mRNA 432273 433147 0.932871 - . ID=Cla000008;
    Chr0 GLEAN CDS 432835 433147 . - 0 Parent=Cla000008;
    Chr0 GLEAN CDS 432273 432742 . - 2 Parent=Cla000008;
    Chr0 GLEAN mRNA 441325 441645 0.999939 + . ID=Cla000009;
    Chr0 GLEAN CDS 441325 441645 . + 0 Parent=Cla000009;
    Chr0 GLEAN mRNA 9242106 9242594 1 + . ID=Cla000010;
    Chr0 GLEAN CDS 9242106 9242160 . + 0 Parent=Cla000010;
    Chr0 GLEAN CDS 9242413 9242594 . + 2 Parent=Cla000010;


    Third column have only CDS or mRNA because it may plant...

    As we can see ftp://www.icugi.org/pub/genome/water...elon_v1.gff.gz, more detailed information can be obtained...

    As a result, I want to know that how to generate gtf file using such gff file.

    (code, methods, anything OK)
    Thanks.~

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
28 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
21 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
38 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
44 views
0 reactions
Last Post SEQadmin2  
Working...