bwtool protocols

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bwtool specifications

Information


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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Documentation


Maintainer


  • person_outline Andy Pohl <>

Additional information


https://github.com/CRG-Barcelona/bwtool/wiki

Publication for bwtool

bwtool in pipelines

 (3)
2018
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 […]

2017
PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] [] defines unmethylated regions (umrs) and lmrs; in this study, we combined both regions into one class, lumrs. any identified regions with more than or equal to 20% dna methylation using bwtool [] were further filtered out. for enhancer identification, regions with both low cg and low chg methylation, which were identified using bedtools [], were called lumrs. the methylation […]

2014
PMCID: 4371841
PMID: 25343476
DOI: 10.7554/eLife.03549.031

[…] for a region from −500 bp to +500 bp of zfp335 chip-seq peaks. dnase i-seq signal and phylop conservation scores for motifs occurring within zfp335 peaks or ±2 kb of refseq tss were aggregated using bwtool. the dnase i digital genomic footprinting (dgf) signal track for mouse thymus was obtained from encode/uw (); sequence conservation tracks were downloaded from ucsc genome browser ()., […]


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bwtool in publications

 (9)
PMCID: 5712219
PMID: 29106418
DOI: 10.1038/ng.3991

[…] nucleosome positioning signals (density graph) of encode cell line gm12878 (lymphoblastoid cell line) were obtained via the ucsc genome browser (http://hgdownload.cse.ucsc.). further, by using the bwtool find program (with parameters local-extrema -maxima -min-sep=150) the nucleosome peak regions were identified across the genome and 146bp flanking the peak (73bp per side) were considered […]

PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] [] defines unmethylated regions (umrs) and lmrs; in this study, we combined both regions into one class, lumrs. any identified regions with more than or equal to 20% dna methylation using bwtool [] were further filtered out. for enhancer identification, regions with both low cg and low chg methylation, which were identified using bedtools [], were called lumrs. the methylation […]

PMCID: 5123355
PMID: 27887606
DOI: 10.1186/s12943-016-0560-0

[…] regulatory regions (crrs) for further analysis. dnasei-seq signal intensities for each crr in the 14 cell types (table ) were computed from the uniformly processed and normalised signal tracks using bwtool []., rna-seq (whole-cell polya+) transcript quantifications were downloaded from the encode dcc portal of ucsc genome browser []. the expression for any transcript whose coordinates […]

PMCID: 5114649
PMID: 27857184
DOI: 10.1038/srep37324

[…] testing using bonferroni correction. the log2 ratios of bi-esctsss to each background set with peaks were computed as log2(% bi-esctsss with peaks/% background with peaks). for the read depth plots, bwtool was used to extract the yy1 chip-seq and input read depth within 5 kb of the three tss sets from big wig files (bi-esctsss, x_bg and auto_bg). read depth ratio between any two tss sets […]

PMCID: 4937605
PMID: 27391956
DOI: 10.1186/s13059-016-1008-y

[…] bp downstream of the transcription start site (tss) of each gene. a gene tss is defined as the most 5′ base of the gene. phastcons scores [] in this window are averaged from the bigwig file with the bwtool software [] and this average is taken as a measure of promoter sequence conservation., for each base in a 6000-bp window around the tss (±3000 bp) of the human genes of our set of one-to-one […]


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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...