HTSeq protocols

HTSeq specifications

Information


Unique identifier OMICS_05835
Name HTSeq
Alternative name HT-Seq
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Cython, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements PySam
Maintained Yes

Subtools


  • HTSeq-count
  • HTSeq-qa

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Maintainer


  • person_outline Simon Anders <>

Publication for HTSeq

HTSeq IN pipelines

 (641)
2018
PMCID: 5754050
PMID: 29300724
DOI: 10.1371/journal.pgen.1007127

[…] genome for sequencing alignment, performed using star (version 2.4.2a) [90]. 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) [91]. the following parameters were specified for the htseq quantification: ‘—format = bam–stranded = no–type = exon’., single cell count data were loaded into the r […]

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

[…] expression levels of 49,585 features annotated in the gencode mouse genome and 92 ercc features were determined using htseq (version 0.6.1p1) [91]. 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 (r version 3.4.0) as a sceset object using the scater package (version […]

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

[…] high throughput dna sequencing were created and reads were mapped onto mm10 assembly of mouse genome using tophat v2.0.14 (kim et al., 2013). quantification of gene expression was performed using htseq v0.6.1 (anders and huber, 2010) 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: 5763955
PMID: 29321057
DOI: 10.1186/s40168-017-0386-z

[…] 2500 sequencer. quality control (qc) was done with fastqc v.0.11.5. reads were mapped with tophat2 v.2.0.11. biological qc was done with picardtools v.1.141. reads per gene feature were counted with htseq v.0.6p1. normalization was performed according to the design model with r/bioconductor edger v. 3.4.2. gene ontology analysis was performed using significantly upregulated mrnas (iav vs. mock, […]

2018
PMCID: 5775430
PMID: 29352240
DOI: 10.1038/s41598-018-19754-8

[…] identified significant degs between groups, many genes with similar expression pattern among different groups were filtered out due to insignificance. therefore, we normalized the read counts from htseq using the deseq. 2 package, and performed weighted gene co-expression network analysis (wgnca) to cluster genes into different modules based on their expression patterns. a total of 19 modules […]

HTSeq institution(s)
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

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