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RegTools specifications


Unique identifier OMICS_32318
Name RegTools
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A reference genome and transcriptome.
Input format FASTA+GTF
Operating system Unix/Linux
Programming languages C, C++, Python, Shell (Bash)
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Malachi Griffith
  • person_outline Yang-Yang Feng

Additional information

Publication for RegTools

RegTools citations


The complexity of titin splicing pattern in human adult skeletal muscles

PMCID: 5874998
PMID: 29598826
DOI: 10.1186/s13395-018-0156-z

[…] the ENCODE project (; accession numbers ENCFF219LYV, ENCFF308RYZ, ENCFF569TCU, ENCFF408QZN, and ENCFF064NBB). Junctions were extracted from the available bam-files using regtools (, we analyzed RNA-Seq data from fetal skeletal muscles (accession numbers ENCFF009MKH, ENCFF084FDS, ENCFF121PKV, and ENCFF405BHX), fetal hea […]


Introns provide a platform for intergenic regulatory feedback of RPL22 paralogs in yeast

PLoS One
PMCID: 5755908
PMID: 29304067
DOI: 10.1371/journal.pone.0190685

[…] signed rank test (function wilcox.test()). Splicing efficiency for each intron was calculated as described previously []. Briefly, transreads (reads spanning exon-exon junctions) were extracted using regtools 0.2.0 ( Intron 5’ end base coverage was determined using bedtools 2.25.0 []. Splicing efficiency was then calculated as the ratio of transreads (mRNA) to intr […]


Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set up

J Biol Eng
PMCID: 5317050
PMID: 28239411
DOI: 10.1186/s13036-017-0050-y

[…] istortion of the signal introduced by the camera was defined accordingly (Fig ). During the parameters identification process, the Tikhonov regularization method, as implemented in the Matlab toolbox regtools [], was used with a threshold automatically selected using the L-plot. This approach is part of the MUSIQ calibration script.Fig. 3 […]


Workflow for Genome Wide Determination of Pre mRNA Splicing Efficiency from Yeast RNA seq Data

Biomed Res Int
PMCID: 5168555
PMID: 28050562
DOI: 10.1155/2016/4783841

[…] Putative splicing events were detected by regtools 0.2.0 ( These tools look for presumed transreads (reads spanning exon-exon junction) in BAM files, compile a table of all identified putative splic […]


Evolution of Intra specific Regulatory Networks in a Multipartite Bacterial Genome

PLoS Comput Biol
PMCID: 4560400
PMID: 26340565
DOI: 10.1371/journal.pcbi.1004478

[…] , regulatory motif files and search and analysis scripts are available as separate git repositories. The rhizoreg repository (, contains the input data; the regtools repository ( contains the main scripts used to conduct the analysis. […]


Molecular characterisation of the NSP4 gene of group A human rotavirus G2P[4] strains circulating in São Paulo, Brazil, from 1994 and 2006 to 2010

PMCID: 4667582
PMID: 26517658
DOI: 10.1590/0074-02760150199
call_split See protocol

[…] uencing files were analysed and aa alignments were constructed using BioEdit v.7.1.9 (). All of the consensus sequences were submitted for genotyping analysis using the web-based tool RotaC () ( These sequences are available in the GenBank database under the accessions KC822323-KC822362.Phylogenetic analyses were performed using MEGA v.6 () and the genetic distances were calcula […]


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RegTools institution(s)
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA; Department of Head and Neck Surgical Oncology, Dana-Farber Cancer Institute, Brigham & Women’s Hospital, Boston, MA, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
RegTools funding source(s)
Supported by the ‘Burroughs Wellcome Fund Institutional Program Unifying Population and Laboratory Based Sciences Award’ at Washington University, the Siteman Cancer Center under fund number #3477-92400, grants from the National Cancer Institute (NCI) of the NIH under award numbers K22CA188163 and U01CA209936 and a grant from the National Human Genome Research Institute (NHGRI) of the NIH under award number R00HG007940.

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