Gffread problems with CHO K1 gff3 file

Kaas

Member

Join Date: Dec 2012

Posts: 20
- Share
- Tweet
#1

Gffread problems with CHO K1 gff3 file

12-21-2012, 05:30 AM

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

test.zip (4.9 KB, 35 views)
Tags: None

Previous template Next

Understanding Genetic Influence on Infectious Disease

by seqadmin

During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
- Channel: Articles
09-09-2024, 10:59 AM
Addressing Off-Target Effects in CRISPR Technologies

by seqadmin

The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality¹. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes². This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways³. Identifying the full range...
- Channel: Articles
08-27-2024, 04:44 AM

Topics	Statistics	Last Post
Study Highlights Challenges in Cellular Reprogramming for Regenerative Medicine by seqadmin Started by seqadmin, Today, 06:25 AM	0 responses 9 views 0 likes	Last Post by seqadmin Today, 06:25 AM
New DNA Modification Discovered as Key to Gene Activation in Early Development by seqadmin Started by seqadmin, Yesterday, 01:02 PM	0 responses 8 views 0 likes	Last Post by seqadmin Yesterday, 01:02 PM
Wastewater Analysis Unlocks New Method for Identifying Public Health Threats by seqadmin Started by seqadmin, 09-18-2024, 06:39 AM	0 responses 10 views 0 likes	Last Post by seqadmin 09-18-2024, 06:39 AM
Molecular Markers Shared Across Dementias by seqadmin Started by seqadmin, 09-11-2024, 02:44 PM	0 responses 13 views 0 likes	Last Post by seqadmin 09-11-2024, 02:44 PM

Seqanswers Leaderboard Ad

Announcement

Gffread problems with CHO K1 gff3 file

Latest Articles

ad_right_rmr

News