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RUM | Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper

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Allows users to align, and quantify feature about Illumina RNA-Seq data. RUM can be used for DNA sequencing and microarray probe mapping. This alignment pipeline is able to map reads in three phases: (1) it maps against the genome using Bowtie; (2) it maps against a transcriptome database using Bowtie; and (3) it maps against the genome using Blat.

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RUM forum

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RUM classification

RUM specifications

Unique identifier:
OMICS_01249
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
Perl, Python
Version:
v2.0.5_06
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable

RUM distribution

versioning

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No versioning.

RUM support

Documentation

Maintainers

Additional information

https://github.com/itmat/rum

Credits

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Publications

Institution(s)

Penn Center for Bioinformatics, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, Philadelphia, PA, USA; Department of Genetics, Philadelphia, PA, USA; F.M. Kirby Center for Molecular Ophthalmology, Philadelphia, PA, USA; Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA

Funding source(s)

Supported by the National Institutes of Health (EY020902 and EY12910; F32 EY020747); Foundation Fighting Blindness, USA; Rosanne Silbermann Foundation; Penn Genome Frontiers Institute; Institute for Translational Medicine and Therapeutics; EuPath DB Project.

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