dexseq_count.py vs htseq-count

Petros84

Junior Member

Join Date: Oct 2014

Posts: 1
- Share
- Tweet
#1

dexseq_count.py vs htseq-count

10-17-2014, 06:56 AM

Dear All,

I have some RNA paired-end files which I have used tophat to allign

~/tophat-2.0.7.Linux_x86_64/./tophat -p10 --segment-length 18
--no-coverage-search --segment-mismatches 1 -G

then samtools

samtools sort -n /media//PRE_6_8_2/accepted_hits.bam
/media/PRE_6_8_2/PRE_6_8_2.sort.hg19.bam

and then

samtools view /media/PRE_6_8_2/PRE_6_8_2.sort.hg19.bam.bam
/media/PRE_6_8_2/PRE_6_8_2.sort.hg19.sam

then I am trying to use DEXSeq and using the

python2.7 /home/3.0/DEXSeq
/python_scripts/dexseq_count.py -p yes -r name -s no
/media/PRE_6_8_2/hg19/hg19_IlluminaAnnotation_genes.gtf
/media/PRE_6_8_2/PRE_6_8_2.sort.hg19.sam
/media/PRE_6_8_2//PRE_6_8_2/untreated1fb.txt

and gives me

_ambiguous 0
_empty 39845364
_lowaqual 0
_notaligned 0

without any reads for any exons. 0 for everything

whereas by using the htseq-count -r name -s no everything looks fine (reads in genes)...

could you please advice me how to solve it? I really need to run the DEXseq as I want reads per exon to detect splice differences.

Thank you in advance for your help

Last edited by Petros84; 10-17-2014, 06:59 AM.
Tags: None

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
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, Today, 10:08 AM	0 responses 6 views 0 reactions	Last Post 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 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 31 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

Unconfigured Ad

dexseq_count.py vs htseq-count

Latest Articles

ad_right_rmr

News