deepTools protocols

deepTools specifications

Information


Unique identifier OMICS_08441
Name deepTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data BAM, bigWig, bedGraph, BED
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • bamCoverage

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Versioning


Add your version

Maintainer


  • person_outline Thomas Manke <>

Additional information


http://deeptools.readthedocs.io/en/latest/

Information


Unique identifier OMICS_08441
Name deepTools
Interface Web user interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data BAM, bigWig, bedGraph, BED
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • bamCoverage

Maintainer


  • person_outline Thomas Manke <>

Additional information


http://deeptools.readthedocs.io/en/latest/

Publication for deepTools

deepTools IN pipelines

 (9)
2018
PMCID: 5770421
PMID: 29339748
DOI: 10.1038/s41467-017-02759-8

[…] g the bowtie2 align program, and data normalization analysis was performed using the macs2 peak calling program. log2 values between mutant 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 = […]

2018
PMCID: 5873942
PMID: 29590119
DOI: 10.1371/journal.pone.0193126

[…] [11]., genome-wide peak coverage analysis and average occupancy profile for nf90/nf110 chip-seq data was performed in r with the chipseeker package and deeptools [74, 75]. motif enrichment analysis and gene annotation of nf90/nf110 chip-seq peaks were computed using hypergeometric optimization of motif enrichment (homer) [76]. nf90/nf110 occupancy […]

2018
PMCID: 5919780
PMID: 29656924
DOI: 10.1016/j.molcel.2018.03.010

[…] ken dbox 2 a this study prs414+-700 sen1-δ485-505 this study p258 this study software and algorithms tophat2 kim et al. (2013) htseq package anders et al., (2015) deeptools ramírez et al. (2014) fimo grant et al. (2011) , further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, […]

2017
PMCID: 5570135
PMID: 28472469
DOI: 10.1093/nar/gkx355

[…] the ensembl 78 release was used. to generate average piwi log2(dam-piwi/dam) profile around tsss, the profiles within the regions of −1.5 to +1.5 kb around tsss of all genes were averaged using ‘deeptools2’ (36), regardless of whether they are in or out of piwi domains. to generate piwi-damid profiles for the te families, the damid-seq reads were mapped onto 100-nt bins of tes consensus […]

2016
PMCID: 4778673
PMID: 26981424
DOI: 10.1016/j.gdata.2016.02.003

[…] [10] using the default parameters with the options “--best” and “-m 1” to retain only uniquely mapped reads. replicate reproducibility was tested using bamcorrelate from the ngs analysis suite deeptools [13], with the custom options bamcorrelate bins --fragmentlength 200 --cormethod pearson. pair of replicates displayed pearson correlation coefficients > 0.80 and therefore […]

deepTools institution(s)
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg, Freiburg, Germany
deepTools funding source(s)
German Research Foundation [SFB 992, Project Z01]; German Epigenome Programme DEEP [01KU1216G]

deepTools review

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Gyan Prakash Mishra

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Desktop
you have NGS datasets?, wanna know how your data looks like? visualize and explore your sequencing data in terms of correlation, heatmap, BedGraph file to visualize in IGV. This is the best tool.