AlleleSeq protocols

AlleleSeq specifications


Unique identifier OMICS_05503
Name AlleleSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Joel Rozowsky <>

Publication for AlleleSeq

AlleleSeq IN pipeline

PMCID: 4512258
PMID: 26140685
DOI: 10.7554/eLife.07860.022

[…] polymorphisms (snps and indels, obtained from the mouse genome project: into the mus musculus grcm38 reference genome sequence using the alleleseq package (rozowsky et al., 2011). we then mapped each of the cast/eij√óc57bl/6j hybrid rna-seq libraries to the splice-junction aware diploid genome using star rna-seq aligner (dobin et al., […]

AlleleSeq institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA

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