RUM protocols

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

 (4)
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).32 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 [25]. differential gene expression analysis was performed using edger [26], 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 [18] 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 […]

2013
PMCID: 3902954
PMID: 24165879
DOI: 10.1093/nar/gkt995

[…] concentration of 2 nm, and sequenced on an illumina platform. sequence reads were mapped against the mus musculus genome assembly (genome reference consortium grcm38, ucsc version mm10) using the rum v. 2.04 pipeline (15). gene expression (reads per kilobase per million mapped reads, rpkm) calculations were performed using rpkmforgenes.py (16). the mm10 refgene.txt-file was downloaded […]

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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