HTSeq protocols

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HTSeq specifications

Information


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
Requirements
PySam
Maintained Yes

Subtools


  • HTSeq-count
  • HTSeq-qa

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Versioning


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Maintainer


  • person_outline Simon Anders <>

Additional information


https://htseq.readthedocs.io/en/release_0.9.1/

Publication for HTSeq

HTSeq in pipelines

 (1036)
2018
PMCID: 5752201
PMID: 29297464
DOI: 10.7554/eLife.29815.043

[…] genome ef4.72 from ensembl using bowtie version 1.0.0 (rrid:scr_005476) () with parameters ‘-n 0 –l 28 –e 70 –k1 –m 1 --best --strata --sam --nomaqround’. reads were counted per exon using htseq-count (rrid:scr_011867) () with default parameters against ensembl’s matching gtf file for ef4.72 and aggregated on the gene-level. the workflow is summarized in ., analysis of p-body […]

2018
PMCID: 5753437
PMID: 29298676
DOI: 10.1186/s12864-017-4411-1

[…] filtered for ribosomal rna, trimmed and aligned to version 3 of the populus trichocarpa reference genome [–] with star []. the number of reads aligning to annotated gene models was determined using htseq []. read counts were normalized with a variance stabilizing transformation (vst) implemented in the r-package deseq2 []. these gene expression values were used in further downstream analyses., […]

2018
PMCID: 5754050
PMID: 29300724
DOI: 10.1371/journal.pgen.1007127

[…] genome for sequencing alignment, performed using star (version 2.4.2a) []. the expression levels of 49,585 features annotated in the gencode mouse genome and 92 ercc features were determined using htseq (version 0.6.1p1) []. the following parameters were specified for the htseq quantification: ‘—format = bam–stranded = no–type = exon’., single cell count data were loaded into the r environment […]

2018
PMCID: 5758557
PMID: 29354030
DOI: 10.3389/fnmol.2017.00433

[…] for high throughput dna sequencing were created and reads were mapped onto mm10 assembly of mouse genome using tophat v2.0.14 (kim et al., ). quantification of gene expression was performed using htseq v0.6.1 (anders and huber, ) and ensembl release 81 database. supervised statistical analysis for differential gene expression has been performed using r (3.3.2) and the deseq2 bioconductor […]

2018
PMCID: 5758812
PMID: 29311649
DOI: 10.1038/s41598-017-17878-x

[…] and mapped (tophat2 version v2.0.10) against the mouse genome, build mm9. approximately, 85–90% mapping rate was observed. only uniquely mapped reads determined the number of reads per gene (htseq-count script 0.6.1p1). differentially expressed genes, were determined by padj < 0.05 and an absolute fold change >2 (deseq. 2 package v1.4.5) and hierarchical clustering using pearson […]


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HTSeq in publications

 (1958)
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] 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 […]

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

[…] 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 (http://www.huber.embl.de/users/anders/htseq/doc/overview.html) using gene annotation files obtained from illumina (http://cufflinks.cbcb.umd.edu/igenomes.html). rna-seq reads […]

PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1

[…] 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 […]

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

[…] fastq files were mapped against the hg19 human reference genome using tophat version 2.0.6 (http://tophat.cbcb.umd.edu/). 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 […]

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

[…] 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 […]


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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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