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Altrans specifications


Unique identifier OMICS_11335
Name Altrans
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Halit Ongen <>

Publication for Altrans

Altrans in publications

PMCID: 5886097
PMID: 29228364
DOI: 10.1093/hmg/ddx424

[…] in the average level of expression, age is also known to cause changes in the mrna splicing process. to identify changes in splicing with age, we produced quantifications of this process using altrans (), which considers links between reads. we found a total of 904 genes (6.3% of the 14, 261 genes with more than one exon expressed) with at least one of their links spanning from two exons […]

PMCID: 5519721
PMID: 28729732
DOI: 10.1038/s41598-017-05744-9

[…] from the first-phase gtex data in 9 tissues. the sre snps are significantly enriched (empirical p-value < 0.001, n = 1000 random sets) for the best sqtls per exon-exon link identified using altrans, after matching on minor allele frequency (maf), distance to intron/exon boundary, gene size, and extent of ld (see methods). furthermore, the sre snps show a shift towards low p-values […]

PMCID: 5409091
PMID: 28062664
DOI: 10.1093/hmg/ddw417

[…] of lcl data in whole blood carried out at meta-exon level using 384 of the 856 individuals. geuvadis cohort used for asqtl identification; splice-junction quantifications were generated by altrans () from the raw sequence alignments. summary eqtl results include only the eqtl association results per test (where full genotype and expression data were not obtainable)., breakdown […]

PMCID: 4310612
PMID: 25634236
DOI: 10.1371/journal.pgen.1004958

[…] effects., we then analyzed alternative splicing and how it is associated to genetic variation and dna methylation across cell-types. we measured alternative splicing levels using the algorithm altrans (ongen h., dermitzakis e.t., submitted) that is based on quantifying exon-exon links between paired reads (see ). to identify associations between snps and alternative splicing (asqtl, […]

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Altrans institution(s)
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland; Swiss Institute of Bioinformatics, Geneva, Switzerland; Center of Excellence for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia; Biomedical Research Foundation Academy of Athens, Athens, Greece
Altrans funding source(s)
This research is supported by grants from European Commission SYSCOL FP7 (UE7-SYSCOL-258236), European Research Council, Louis Jeantet Foundation, Swiss National Science Foundation, and the NIH-NIMH (GTEx).

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