HTSeq pipeline

HTSeq specifications


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


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  • person_outline Simon Anders <>

Publication for HTSeq

HTSeq citations

PMCID: 5940877

[…] raw sequences were aligned to the drosophila genome (drosophila genome version r5.42) using burrows-wheeler aligner (bwa) software. numbers of reads aligned within each gene were counted using the htseq package of python and normalized with the deseq package of r. differentially expressed genes between w1118 and egg2138/df(2r)dll-mp ovaries were identified using the deseq criteria: normalized […]

PMCID: 5946033

[…] performed as in our previous study (18). for gene expression analysis, the number of reads falling in the meta-gene, which was created by merging exons from all isoforms of a gene, was counted using htseq-count (18). to identify the differentially expressed genes (degs), the deseq2 algorithm was performed, and the genes with a p < 0.05 (paired test) were considered to be significantly […]

PMCID: 5928165

[…] abundance (fragments per kilobase of exon per million fragments mapped (fpkm)) were carried out using cufflinks software. differential gene expression analyses between groups were performed using htseq software for tumor samples66 and deseq2 software for cell line samples67. heatmap.2 in the ‘gplots’ package of the r program was used for the construction of heat maps. genes that were up- […]

PMCID: 5955139

[…] 100 bp sequences were mapped to the hg19 genome with the strongarm pipeline developed for the pcgp project [40] which employs bwa [41] and star [42] aligners. transcript level data was counted using htseq [43]. transcript level log2fpkm (log2(fpkm +0.5)) was calculated and used to define log fold-change and average expression values. transcripts with maximum global expression greater than 1 […]

PMCID: 5911435

[…] to the hg19 build of the reference genome and a pre-built splice junction database generated from known gene models (ucsc genes) using tophat18. counts for each transcript were determined using ht-seq19 and statistical analysis performed using the edger package in r20., for outlier-gene analysis, we calculated the z statistic for each gene by using the ‘scale’ function in r. mean and sd […]

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

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