bwtool protocols

bwtool specifications


Unique identifier OMICS_05125
Name bwtool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BIGWIG, BED
Output format JSP
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Andy Pohl <>

Additional information

Publication for bwtool

bwtool IN pipeline

PMCID: 5770421
PMID: 29339748
DOI: 10.1038/s41467-017-02759-8

[…] and wild-type cells were calculated using bamcompare in the deeptools, a data analysis program for high-throughput sequencing. the read counts and rpkm values were identified using the bedtools and bwtool utility program. rpkm values were calculated as: rpkm = (number of reads mapped to a gene × 1e + 09)/ (length of the gene × number of total mapped read counts in the experiment). the scatter […]

bwtool institution(s)
Department of Gene Regulation, Stem Cells, and Cancer, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain; Department of Experimental and Health Sciences (CEXS), Universitat Pompeu Fabra, Barcelona, Spain
bwtool funding source(s)
Supported by grants from the Departament d’Innovacio Universitat i Empresa (DIUiE) 2009SGR574, Ministerio de Educacion y Ciencia (MEC) BFU2010-01531 and CSD2006-00049.

bwtool review

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Anonymous user #970

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I am using bwtool for more than a year now and I found it extremely useful, full of features, easy to use and extremely fast too...
I highly recommended...