RUM protocols

RUM statistics

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RUM specifications

Information


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

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Additional information


https://github.com/itmat/rum

Publication for RUM

RUM in pipelines

 (6)
2017
PMCID: 5624912
PMID: 28970527
DOI: 10.1038/s41467-017-01095-1

[…] 2.2.58. base-calling was performed using rta: 1.18.64. data were demultiplexed and bcl files converted to fastq using bcl2fastq 2.17.1.14. 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, […]

2016
PMCID: 5190055
PMID: 27248322
DOI: 10.18632/oncotarget.9666

[…] provided in the kit were used., all the rna-seq libraries were sequenced by the functional genomics core at the university of pennsylvania. sequencing reads were aligned to the ucsc hg19 using rum pipeline and differential gene expression analysis were performed using edger [, ]. as an unbiased interrogation of gene regulation, differentially expressed genes (fdr < 0.0001, […]

2015
PMCID: 4698881
PMID: 26740970
DOI: 10.1016/j.jcmgh.2015.06.007

[…] low-quality reads as well as ribosomal and repeat sequences were filtered out. remaining reads were aligned to the mouse reference genome (ncbi build 37, mm9) using rna-seq unified mapper (rum) alignment software (university of pennsylvania school of medicine, philadelphia, pa). differential expression analysis was carried out using edger software (walter and eliza hall institute […]

2015
PMCID: 4703852
PMID: 26844207
DOI: 10.1016/j.molmet.2015.11.001

[…] 2000. all the high throughput sequencing was performed by the functional genomics core at the university of pennsylvania using hiseq 2000 or 2500. rna-seq reads were aligned to the ucsc mm9 using rum . differential gene expression analysis was performed using edger , where differentially regulated genes with fdr < 0.05 were selected for downstream analysis. hierarchical clustering […]

2013
PMCID: 3808424
PMID: 24205000
DOI: 10.1371/journal.pone.0077859

[…] ma). two libraries for each condition (control and hypoxia-treated) were sequenced using a 2x36 cycle paired-end run on illumina genome analyzer iix. the resulting reads were mapped using the rum alignment package [] with default settings to the mouse reference genome mm9. the aligned reads were then processed with htseq-count to count the number of reads mapped to genes defined […]


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RUM in publications

 (24)
PMCID: 5738376
PMID: 29263354
DOI: 10.1038/s41598-017-18236-7

[…] 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 […]

PMCID: 5697891
PMID: 29121637
DOI: 10.1371/journal.pgen.1007033

[…] #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., […]

PMCID: 5658171
PMID: 29073251
DOI: 10.1371/journal.ppat.1006678

[…] 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 […]

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

[…] 2.2.58. base-calling was performed using rta: 1.18.64. data were demultiplexed and bcl files converted to fastq using bcl2fastq 2.17.1.14. 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, […]

PMCID: 5319189
PMID: 28219335
DOI: 10.1186/s12870-017-0996-4

[…] t; 0.05, |∆isoform fraction | ≥0.1, and mean fpkm of control or test group ≥1), and predict nonsense-mediated decay (nmd) sensitive transcripts., in the second approach, alignment was performed using rum 2.0.4 (default parameters) [] keeping only uniquely mapped reads. deseq2 [] was used for gene count normalization and to identify differentially expressed genes (fdr < 0.05, |log2(fold change)| […]


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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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