Rf at 12:22, 14 June 2017

2017-06-14T12:22:11Z

Rf: Created page with "= Introduction = Deeptools is a python processing suite for bamfiles and renders them into genome browser track forms as such as bed and bigwig. It can be invoked in three w..."

2017-06-14T12:20:01Z

Created page with "= Introduction = Deeptools is a python processing suite for bamfiles and renders them into genome browser track forms as such as bed and bigwig. It can be invoked in three w..."

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= Introduction =

Deeptools is a python processing suite for bamfiles and renders them into genome browser track forms as such as bed and bigwig.

It can be invoked in three ways, from the command line, using Galaxy or via an API against which you would write python scripts.

= Help output =

$ deeptools -h
usage: deeptools [-h] [--version]

deepTools is a suite of python tools particularly developed for the efficient analysis of
high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

Each tool should be called by its own name as in the following example:

$ bamCoverage -b reads.bam -o coverage.bw

If you find deepTools useful for your research please cite as:

Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert,
Andreas S. Richter, Steffen Heyne, Friederike Dündar,
and Thomas Manke. 2016. "deepTools2: A next Generation Web Server for Deep-Sequencing
Data Analysis." Nucleic Acids Research, April. doi:10.1093/nar/gkw257.

[ Tools for BAM and bigWig file processing ]
multiBamSummary compute read coverages over bam files. Output used for plotCorrelation or plotPCA
multiBigwigSummary extract scores from bigwig files. Output used for plotCorrelation or plotPCA
correctGCBias corrects GC bias from bam file. Don't use it with ChIP data
bamCoverage computes read coverage per bins or regions
bamCompare computes log2 ratio and other operations of read coverage of two samples per bins or regions
bigwigCompare computes log2 ratio and other operations from bigwig scores of two samples per bins or regions
computeMatrix prepares the data from bigwig scores for plotting with plotHeatmap or plotProfile

[ Tools for QC ]
plotCorrelation plots heatmaps or scatterplots of data correlation
plotPCA plots PCA
plotFingerprint plots the distribution of enriched regions
bamPEFragmentSize returns the read length and paired-end distance from a bam file
computeGCBias computes and plots the GC bias of a sample
plotCoverage plots a histogram of read coverage

[Heatmaps and summary plots]
plotHeatmap plots one or multiple heatmaps of user selected regions over different genomic scores
plotProfile plots the average profile of user selected regions over different genomic scores
plotEnrichment plots the read/fragment coverage of one or more sets of regions

[Miscellaneous]
computeMatrixOperations Modifies the output of computeMatrix in a variety of ways.

For more information visit: http://deeptools.readthedocs.org

optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit

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	It can be invoked in three ways, from the command line, using Galaxy or via an API against which you would write python scripts.		It can be invoked in three ways, from the command line, using Galaxy or via an API against which you would write python scripts.
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		+	Its command-line tools do not work via the subcommand convention but have their own principle command.

	= Help output =		= Help output =

Deeptools - Revision history

Rf at 12:22, 14 June 2017

Rf: Created page with "= Introduction = Deeptools is a python processing suite for bamfiles and renders them into genome browser track forms as such as bed and bigwig. It can be invoked in three w..."