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/

deepTools article

deepTools citations

 (3)
2017
PMCID: 5468370

[…] above threshold. the counts by exon data were used to determine the number of exons detected. correlation and gene coverage plots were generated using log2 normalized counts with r (v3.3.0) and deeptools (ramírez et al., 2014), respectively. gene coverage profiles include the top 4000 expressed genes excluding rrna and mitochondrial genes encoded on chromosome m. for the gene coverage […]

2017
PMCID: 5436145

[…] using picardtools (http://picard.sourceforge.net) and reads mapping in blacklisted region defined by the encode consortium filtered using bedtools56. tag density profiles were generated using deeptools bamcoverage57 and a smoothing kernel with a 50-bp bandwidth. cross-correlation was computed as described previously31. for each chromosome , the tag count vectors and were calculated […]

2017
PMCID: 5295818

[…] background and therefore was performed using the chip sample only at a false discovery rate of less than 0.05. aggregation plots, tag heat maps, and global correlation analyses were performed using deeptools 2.0 (ramírez et al., 2014). biochip-seq signal was visualized in the integrated genome viewer (thorvaldsdóttir et al., 2013)., to associate genomic regions to genes, we used homer’s […]

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.