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HTSeq specifications


Unique identifier OMICS_05835
Name HTSeq
Alternative name HT-Seq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Cython, Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.11.0
Stability Stable
Maintained Yes


  • HTSeq-count
  • HTSeq-qa




No version available


  • person_outline Simon Anders

Additional information

Publication for HTSeq

HTSeq citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] high-quality reads were mapped via STAR (version 2.5.0b) against the mouse (GRCm38) reference genome. After processing of the alignment results with SAMtools (0.1.19) counts per gene were obtained by HTSeq (version 0.6.0). Normalization and differential expression analysis between two samples was carried out with DESeq2. For the visualization of gene expression and unsupervised hierarchical cluste […]


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] were obtained using the MAP-RSeq v.1.2.1 workflow, the Mayo Bioinformatics Core pipeline. MAP-RSeq consists of alignment with TopHat 2.0.6 against the human hg19 genome build and gene counts with the HTSeq software 0.5.3p9 ( using gene annotation files obtained from Illumina ( RNA-seq reads w […]


FACS Seq analysis of Pax3 derived cells identifies non myogenic lineages in the embryonic forelimb

Sci Rep
PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1
call_split See protocol

[…] ed and analyzed with the same methods. After filtering low quality reads TopHat version 2.1.0 was used to align all reads to the mm10 genome with default parameters and to identify splice junctions,. HTseq was used to create count tables from tophat2 aligned reads. DESeq2 was used to calculate differential gene expression between time points using an FDR adjusted cutoff of p ≤ 0.05, with a fold ch […]


Genomic alterations of ground glass nodular lung adenocarcinoma

Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] e FASTQ files were mapped against the hg19 human reference genome using TopHat version 2.0.6 ( Raw read counts mapped onto genes were measured with the BAM format file by HTSeq version 0.6.1. Then a total of 18,161 coding genes were subjected to measurement of the transcript abundance, and low expressed genes were filtered out using the criterion of a maximum read coun […]


Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y
call_split See protocol

[…] Raw reads were aligned to the human reference genome hg19 and mouse reference genome mm8, respectively, using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjami […]


Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast like synoviocytes

Nat Commun
PMCID: 5953939
PMID: 29765031
DOI: 10.1038/s41467-018-04310-9

[…] aw RNA-seq reads. After trimming, reads with less than 30 bp were further discarded. The remaining reads were aligned to human reference genome hg19 using STAR (2.3.0) and assembled and quantified by HTSeq (0.5.4p5). DEGs were identified using DESeq2 package in R. To be considered a DEG, twofold change of gene expression levels between RA and OA should be achieved and the B-H adjusted p-value is < […]


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HTSeq institution(s)
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
HTSeq funding source(s)
Supported by the European Union via the 6th Framework Programme network Chromatin Plasticity (Project no. 35733) and 7th Framework Programme project Radiant (Project no. 305626).

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