Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • Kaas
    Member
    • Dec 2012
    • 20
    #1

    Gffread problems with CHO K1 gff3 file

    I am very much a newbie in this field but a part of my PhD project is to analyze data i have generated on 14 CHO DUKX strains. Right now I am just setting up the system and has so far found the CHO K1 genome and gff3 files.

    But when i check the annotation file by the cufflink tool gffread is outputs

    csrk@davinci:~/genome> gffread -E CHOK1.gff3 -o- | more
    Error: duplicate GFF ID 'rna1362' encountered!
    Error: duplicate GFF ID 'rna2220' encountered!
    Error: duplicate GFF ID 'rna2366' encountered!
    Error: duplicate GFF ID 'rna3249' encountered!
    Error: duplicate GFF ID 'rna7611' encountered!
    Error: duplicate GFF ID 'rna7612' encountered!
    Error: duplicate GFF ID 'rna7613' encountered!
    Error: duplicate GFF ID 'rna7615' encountered!
    Error: duplicate GFF ID 'rna7626' encountered!
    Error: duplicate GFF ID 'rna9416' encountered!
    Error: duplicate GFF ID 'rna11285' encountered!
    Error: duplicate GFF ID 'rna11287' encountered!
    Error: duplicate GFF ID 'rna15111' encountered!
    Error: duplicate GFF ID 'rna18225' encountered!
    Error: duplicate GFF ID 'rna18229' encountered!
    Error: duplicate GFF ID 'rna18230' encountered!
    Error: duplicate GFF ID 'rna18861' encountered!
    Error: duplicate GFF ID 'rna18862' encountered!
    Error: duplicate GFF ID 'rna19473' encountered!
    Error: duplicate GFF ID 'rna19903' encountered!
    Error: duplicate GFF ID 'rna20504' encountered!

    when I search for one of the RNA's it outputs more than 500 lines containing more than 10 different gene-names.
    What needs to be changes in the gff3 file before cufflinks (or e.g. HTseq) will be able to use it?

    output search for rna1362 is attached

    Merry Christmas
    Attached Files
    Tags: None
Previous template Next

Latest Articles

Collapse
  • SEQadmin2
    Cancer Drug Resistance: The Lingering Barrier to Rising Survival
    by SEQadmin2



    Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

    There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
    Today, 05:17 AM
  • GATTACAT
    Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by GATTACAT
    Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
    07-01-2026, 11:43 AM
  • SEQadmin2
    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by SEQadmin2


    I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

    Here are nine questions we think about, in roughly the order they matter, before...
    06-18-2026, 07:11 AM
View All

ad_right_rmr

Collapse

News

Collapse
Topics Statistics Last Post
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
Started by SEQadmin2, Today, 10:08 AM
0 responses
5 views
0 reactions
 Last Post SEQadmin2
by SEQadmin2
Today, 10:08 AM  
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
Started by SEQadmin2, Yesterday, 11:05 AM
0 responses
7 views
0 reactions
 Last Post SEQadmin2
by SEQadmin2
Yesterday, 11:05 AM  
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
Started by SEQadmin2, 07-02-2026, 11:08 AM
0 responses
29 views
0 reactions
 Last Post SEQadmin2
by SEQadmin2
07-02-2026, 11:08 AM  
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2
Started by SEQadmin2, 06-30-2026, 05:37 AM
0 responses
28 views
0 reactions
 Last Post SEQadmin2
by SEQadmin2
06-30-2026, 05:37 AM  
View All
Working...