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RNA-Seq Unified Mapper

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013a-3178-df7b-01af-beb880000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Resource Description
    "RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. RUM can also be used effectively for DNA sequencing (e.g. ChIP-Seq) and microarray probe mapping. RUM also has a strand specific mode. RUM is highly configurable, however it does not require fussing over options, the defaults generally give good results." "RUM maps reads in three phases. First it maps against the genome using Bowtie, then it maps against a transcriptome database using Bowtie, then it maps against the genome using Blat. The information from the three mappings is merged into one mapping. This leverages the advantages of both genome and transcriptome mapping as well as combining the speed of Bowtie with the sensitivity and flexibility of Blat. Coverage plots are generated, normalized intensities for genes, introns and exons are generated, and files describing the junctions are generated. Files are also generated that have the alignment for each read, one per line, in RUM and SAM format."
  2. Additional Name
    RUM
  3. Contact
    Grant, Gregory R., Ph.D.
  4. Used by
    University of Pennsylvania
  5. Data Input
    Nucleotide sequences
  6. Data Output
    Feature counts file
  7. Data Output
    Coverage files
  8. Data Output
    Unique mappers file
  9. Data Output
    Non-unique mappers file
  10. Data Output
    Sequence alignment file
  11. Data Output
    Junction information file
  12. Data Output
    Inferred exons files
  13. Data Output
    Mapping statistics file
  14. Data Output
    RUM parameters settings file
  15. Data Output
    RUM error log file
  16. Software purpose
    Sequence alignment objective
  17. Related Publication or Documentation
    Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
  18. Related Publication or Documentation
    Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
  19. Website(s)
    http://www.cbil.upenn.edu/RUM/userguide.php
  20. Website(s)
    https://github.com/PGFI/rum
  21. Related Technique
    RNA sequencing
  22. Related Technique
    DNA sequencing assay
  23. Developed by
    Pizarro, Angel
  24. Developed by
    Grant, Gregory R., Ph.D.
  25. Developed by
    DeLaurentis, Michael
  26. Software license
    MIT License
  27. Algorithm used
    Burrows-Wheeler technique
  28. Coded in
    Perl
 
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Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016