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ORMAN | Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms

Computes the minimum number of potential transcript products for each gene and to assign each multimapping read to one of these transcripts based on the estimated distribution of the region covering the read. ORMAN achieves this objective through a combinatorial optimization formulation, which is solved through well-known approximation algorithms, integer linear programs and heuristics.

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ORMAN forum

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ORMAN classification

ORMAN specifications

Unique identifier:
OMICS_01284
Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Stability:
Stable
Name:
Optimal Resolution of Multimapping Ambiguity of RNA-Seq Reads
Interface:
Command line interface
Operating system:
Unix/Linux
Version:
1.2
Maintained:
Yes

ORMAN distribution

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ORMAN support

Maintainer

  • S. Cenk Sahinalp <>

Credits

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Publications

Institution(s)

School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA

Funding source(s)

Supported by NSERC Discovery and Discovery Accelerate Grant, Canadian Cancer Society Innovation Grant, Vanier Canada Graduate Scholarship and Ebco/Epic Visiting Chairs and ICGC Grant.

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