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chevron_left Bioinformatics workflows Duplicate read removal Adapter trimming Reference-based transcriptome assembly Spliced read alignment chevron_right

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Horse_Trans specifications


Unique identifier OMICS_15233
Name Horse_Trans
Alternative name Horse Transcriptome
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python, R
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Titus Brown

Publication for Horse Transcriptome

Horse_Trans citations


Identification of long non coding RNA in the horse transcriptome

BMC Genomics
PMCID: 5496257
PMID: 28676104
DOI: 10.1186/s12864-017-3884-2

[…] interpretation of the data or writing of the manuscript., the input data including the scripts used to make them can be found at original equine transcriptome github page: (this repository is archived by zenodo at 10.5281/zenodo.56934). all sequencing reads used in this study have been submitted to ncbi sequence read archive; sra srp082284 for muscle […]


TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA Seq

BMC Genomics
PMCID: 5139010
PMID: 27919223
DOI: 10.1186/s12864-016-3345-3

[…] data represent the first whole transcriptome assembly of the quarter horse genome. with an average of 33.7 million reads per sample, we have generated an average of 53.83x coverage of the quarter horse transcriptome. the cufflinks program estimated over 34,000 genes to be present in the quarter horse genome. furthermore, cufflinks estimated over 74,500 isoforms of these 34,000 genes […]


RNA expression of TLR10 in normal equine tissues

BMC Res Notes
PMCID: 4952062
PMID: 27435589
DOI: 10.1186/s13104-016-2161-9

[…] approval was obtained from the university of nottingham, school of veterinary medicine and science clinical ethical review panel. data from another study (moreton et al. [], characterisation of the horse transcriptome from immunologically active tissues) [] has been re-analysed in this study. permission to reuse this data was obtained from these authors. that study included a small number […]


The Transcriptome of Equine Peripheral Blood Mononuclear Cells

PLoS One
PMCID: 4366165
PMID: 25790166
DOI: 10.1371/journal.pone.0122011

[…] transcript annotated. in contrast, in human 18,516 (82%) from the 22,680 protein coding genes have more than one transcript annotated. therefore, any isoform-specific gene expression analysis of the horse transcriptome, using the currently available set of annotated transcripts, will be based on a highly incomplete annotation. although it is computationally more challenging, the expression […]


Genome Wide Analysis of DNA Methylation before and after Exercise in the Thoroughbred Horse with MeDIP Seq

Mol Cells
PMCID: 4363720
PMID: 25666347
DOI: 10.14348/molcells.2015.2138

[…] in its lines and hypermethylation of ltr elements (). the expression of lines induces genomic instability, with the host cell maintaining the methylation state of the lines (). in the horse transcriptome, line-containing transcripts blood cells were upregulated after exercise, and this study demonstrated that exercise-induced stress leads to change in lines in the host (). […]


Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses

PLoS One
PMCID: 3962374
PMID: 24658125
DOI: 10.1371/journal.pone.0091418

[…] surrounding the selected gene can be found by fine-scale mapping. using such genome scans, selective sweeps have been identified in domestic and natural (wild progenitor) populations , ., previous horse transcriptome studies using rna-seq were carried out by mapping sequence reads to a reference genome. however, reference genome assembly has been known to have flaws including missing expressed […]

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Horse_Trans institution(s)
Department of Population Health and Reproduction, University of California, Davis, CA, USA; Department of Clinical Pathology, College of Medicine, Mansoura University, Egypt, Mansoura, Egypt; Department of Animal Science, University of California, Davis, CA, USA; Veterinary Genetics Laboratory, University of California, Davis, CA, USA; Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA
Horse_Trans funding source(s)
This work was supported by the National Institutes of Health (NIH) (1K01OD015134-01A1 and L40 TR001136), and the Morris Animal Foundation (D14EQ-021).

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