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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


No version available



  • person_outline Halit Ongen

Publication for Altrans

Altrans citations


Age dependent changes in mean and variance of gene expression across tissues in a twin cohort

Hum Mol Genet
PMCID: 5886097
PMID: 29228364
DOI: 10.1093/hmg/ddx424
call_split See protocol

[…] , only exons from protein-coding genes and LincRNAs from verified loci (level 1) and manually annotated (level 2) were investigated. We calculated the relative quantification of splicing events using Altrans (). Read counts assigned to links and exons were scaled to 10 million reads. , Table S7 shows the total number of exons and genes sequenced per tissue, as well as the total number of exons, ge […]


Evidence of selection on splicing associated loci in human populations and relevance to disease loci mapping

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

[…] s (sQTLs) 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 for t […]


Mapping eQTLs with RNA seq reveals novel susceptibility genes, non coding RNAs and alternative splicing events in systemic lupus erythematosus

Hum Mol Genet
PMCID: 5409091
PMID: 28062664
DOI: 10.1093/hmg/ddw417

[…] imputation call-rates < 0.8, and HWE P < 1×10−04. We removed non-uniquely mapped, non-properly paired reads, and reads with more than eight mismatches for read and mate using SAMTools (). We used the Altrans () method against GENCODE v10 to generate relative quantifications (link-counts) of splicing events; which in brief, utilizes split and paired-end reads to count links between exon-boundaries, […]


Tissue Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

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

[…] order to test whether these exons coding for several isoforms and presenting discordant associations were indeed being expressed in different transcripts between fibroblasts and T-cells, we used the Altrans method described below to test for differential exon-exon link usage. We were able to quantify links for 5 of these exons, and found highly significant differential link usage between cell-typ […]


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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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