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RUM specifications


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


No version available



Additional information

Publication for RUM

RUM citations


Involvement of Innate Immune System in Late Stages of Inherited Photoreceptor Degeneration

Sci Rep
PMCID: 5738376
PMID: 29263354
DOI: 10.1038/s41598-017-18236-7
call_split See protocol

[…] d. Reads that aligned to a generic set of sequences containing ribosomal and known repeat sequences in humans were also removed before further analysis of the sequencing data. RNA-seq Unified Mapper (RUM) was used for aligning reads to known transcripts included in RefSeq, UCSC known genes and ENSEMBL transcripts, and to the dog genome. Unique alignments to RefSeq were extracted from the RUM outpu […]


The combinatorial control of alternative splicing in C. elegans

PLoS Genet
PMCID: 5697891
PMID: 29121637
DOI: 10.1371/journal.pgen.1007033
call_split See protocol

[…] cession #PRJNA412927.Each sequenced sample yielded approximately 200 million, 100bp paired-end reads, which were mapped to the WS220 version of the C. elegans genome using the RNA-Seq unified mapper (RUM) program [] at default parameters. Uniquely mapped reads that spanned exon-exon junctions, and were annotated by RUM as “high-quality junctions”, were used to calculate splice junction usage.The d […]


Single cell analysis identifies cellular markers of the HIV permissive cell

PLoS Pathog
PMCID: 5658171
PMID: 29073251
DOI: 10.1371/journal.ppat.1006678
call_split See protocol

[…] nimum length of 2 either at the 5'-end or at the 3’-end. Cleaned reads were aligned to the human reference genome with STAR aligner v2.3.0 [] using the Ensembl gene GRCh37 release 70 annotation file. RUM aligner [] was used for the first 8 bulk libraries indicated in . The number of reads per gene was quantified with HTSeq-count v.0.6.1 [], with parameters mode = union and type = exon. An average […]


Transcriptomes and neurotransmitter profiles of classes of gustatory and somatosensory neurons in the geniculate ganglion

Nat Commun
PMCID: 5624912
PMID: 28970527
DOI: 10.1038/s41467-017-01095-1

[…] tware 2.2.58. Base-calling was performed using RTA: 1.18.64. Data were demultiplexed and BCL files converted to FASTQ using bcl2fastq Sequence data were processed at the NGSC through their RUM package v2.0.5_06 for genome alignment, junction calling, and feature quantification. Reads were mapped against mouse transcriptome (mm9) using Bowtie and against genome using Bowtie and Blat, and […]


DART: a fast and accurate RNA seq mapper with a partitioning strategy

PMCID: 5860201
PMID: 28968831
DOI: 10.1093/bioinformatics/btx558

[…] e junctions.Various de novo spliced RNA aligners have been developed in recent years, which include QPALMA (), TopHat (), GSNAP () (and GSTRUCT is its successive version), PALMapper (), MapSplice (), RUM(), GEM (), STAR(), TopHat2 (), HISAT () and Subread (). In summary, most of the short read aligners basically adopt the seed-and-extend strategy (), which is sequential in nature and takes much lo […]


DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates

PMCID: 5870796
PMID: 28595376
DOI: 10.1093/bioinformatics/btx357

[…] eir matched adjacent normal tissues (; ). The mRNA of each sample was extracted, amplified and sequenced. 150 base paired-end reads were generated and aligned to the hg19 human reference genome using RUM (RNA-Seq Unified Mapper) (). The aligned reads are used as input to three methods, Cuffdiff, RSEM-EBSeq, BitSeqVB, and DEIsoM, for DE isoform detection. MISO is not included because it cannot perf […]


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RUM 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
RUM 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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