RMAP statistics

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Citations per year

Citations chart

Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

RMAP specifications


Unique identifier OMICS_00681
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Reads files and chromosome files.
Output format BED
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.05
Maintained No



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Additional information

Previous version: http://rulai.cshl.edu/rmap/rmap1-webpage/index.shtml

Publications for RMAP

RMAP in publications

PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] reference genomes or transcriptomes. the most commonly used mapping algorithms used for this task include bowtie [], bowtie2 [], star [], novoalign (http://www.novocraft.com/products/novoalign/), rmap [], tophat [], gsnap [], soap [] and bwa [], some with unique advantages over others depending on whether mapping is done on a genome versus transcriptome. the choice of algorithm […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] aligners, have been developed to map the bs-seq short reads (). due to the specificity of the bs-seq reads, some general aligners are developed with bs-seq modules (such as gsnap, last, novoalign, rmap, and segemehl). specific bs-seq aligners were also developed to map the bs-seq reads. among these tools, two alternative approaches have been widely used. the three-letter aligners (such […]

PMCID: 4896272
PMID: 26961371
DOI: 10.1186/s12859-016-0910-3

[…] the problem of efficiently dealing with the high number of c-to-t mismatches. a different approach—to allow c-to-t mismatches by using wild-card techniques—is adopted by tools such as bsmap [] and rmap []. a mixture of the two strategies is also possible: the bs-aligner erne-bs5 (version 1) [] uses a bisulfite-aware hash function invariant under bisulfite-induced mismaches, thus avoiding […]

PMCID: 4009243
PMID: 24839440
DOI: 10.1155/2014/472045

[…] (i.e., the percentage of reads that are mapped to a reference genome)., many tools have been developed to tackle this computational challenge such as maq [], bismark [], bsmap [], pash [], rmap [], gsnap [], novoalign [], bfast [], brat-bw [], methylcoder [], cokusalignment [], bs-seeker [], bs-seeker2 [], segemehl [], biss [], batmeth [], and the latest one erne-bs5 []. the majority […]

PMCID: 3980841
PMID: 24779008
DOI: 10.1155/2014/309650

[…] ngs platforms. according to the popularity of multiple aligners (see supplementary file 3 in supplementary material available online at http://dx.doi.org/10.1155/2014/309650), the aligners, like rmap, seqmap, maq, shrimp2, bwa, soap2, and bowtie, are popular for illumina platform. rmap, shrimp2, bwa, soap2, bowtie, and ssaha2 are widely applied for roche 454, while rmap, maq, shrimp2, bwa, […]

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RMAP institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
RMAP funding source(s)
Supported by National Institutes of Health (U01 ES017166 and T32 CA00917631), Department of the Army (W81XWH04-1-0477), The Breast Cancer Research Foundation and Howard Hughes Medical Institute.

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