Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 11:49 AM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 08:47 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Working...
X