about DEG after cuffdiff

Hoseong choi

Junior Member

Join Date: Apr 2014

Posts: 1
- Share
- Tweet
#1

about DEG after cuffdiff

04-21-2014, 10:11 PM

hi all.

i am working on soybean gene expression analysis with tophat/cuffdiff

After cuffdiff run, I could get results about expression of genes from gene_exp.diff file

In some case, I could not determine the exact expression of gene.

For example,

Glyma03g03100.2:1-1121 Healthy 24hpi OK 37.9054 13.4419 -1.49567 -2.46173 0.04 0.769321 no
Glyma03g03100.2:1181-1853 Healthy 24hpi OK 43.4734 13.3734 -1.70077 -2.93749 0.02925 0.658614 no

Glyma03g03100.2 is one gene. According to results, expression of this gene is divided into 2 fragment.

In this case, how can I analysis gene expression of Glyma03g03100??
Tags: cuffdiff
dpryan

Devon Ryan

Join Date: Jul 2011

Posts: 3478
- Share
- Tweet
#2

04-22-2014, 12:16 AM

Did this happen with all genes or just this one?

I'm guessing that you supplied cufflinks with an annotation file (probably in GTF format). Can you post the lines relevant to that gene? I'm guessing that cufflinks got confused by the formatting for some reason and computed metrics per-exon, rather than per-gene/transcript.
Comment

Previous template Next

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...
- Channel: Articles
Today, 05:17 AM
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.
- Channel: Articles
07-01-2026, 11:43 AM
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...
- Channel: Articles
06-18-2026, 07:11 AM

Topics	Statistics	Last Post
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 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 28 views 0 reactions	Last Post 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 by SEQadmin2 06-30-2026, 05:37 AM
Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2 Started by SEQadmin2, 06-26-2026, 11:10 AM	0 responses 27 views 0 reactions	Last Post by SEQadmin2 06-26-2026, 11:10 AM

Unconfigured Ad

about DEG after cuffdiff

Comment

Latest Articles

ad_right_rmr

News