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deepTools

Supported Tool

Tools to process and analyze deep sequencing data.

Description

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

The MultiQC module for deepTools parses a number of the text files that deepTools can produce. In particular, the following are supported:

  • bamPEFragmentSize --table
  • bamPEFragmentSize --outRawFragmentLengths
  • estimateReadFiltering
  • plotCoverage ---outRawCounts (as well as the content written normally to the console)
  • plotEnrichment --outRawCounts
  • plotFingerprint --outQualityMetrics --outRawCounts
  • plotPCA --outFileNameData
  • plotCorrelation --outFileCorMatrix
  • plotProfile --outFileNameData

Please be aware that some tools (namely, plotFingerprint --outRawCounts and plotCoverage --outRawCounts) are only supported as of deepTools version 2.6. For earlier output from plotCoverage --outRawCounts, you can use #'chr' 'start' 'end' in search_patterns.yaml (see here for more details). Also for these types of files, you may need to increase the maximum file size supported by MultiQC (log_filesize_limit in the MultiQC configuration file). You can find details regarding the configuration file location here.

Note that sample names are parsed from the text files themselves, they are not derived from file names.

File search patterns

deeptools/bamPEFragmentSizeTable:
  contents: "\tFrag. Sampled\tFrag. Len. Min.\tFrag. Len. 1st. Qu.\tFrag. Len.
    Mean\tFrag. Len. Median\tFrag. Len. 3rd Qu."
  num_lines: 1
deeptools/bamPEFragmentSizeDistribution:
  contents: "#bamPEFragmentSize"
  num_lines: 1
deeptools/estimateReadFiltering:
  contents: Sample	Total Reads	Mapped Reads	Alignments in blacklisted
    regions	Estimated mapped reads
  num_lines: 1
deeptools/plotCorrelationData:
  contents: "#plotCorrelation --outFileCorMatrix"
  num_lines: 1
deeptools/plotCoverageStdout:
  contents: sample	mean	std	min	25%	50%	75%	max
  num_lines: 1
deeptools/plotCoverageOutRawCounts:
  contents: "#plotCoverage --outRawCounts"
  num_lines: 1
deeptools/plotEnrichment:
  contents: file	featureType	percent	featureReadCount	totalReadCount
  num_lines: 1
deeptools/plotFingerprintOutRawCounts:
  contents: "#plotFingerprint --outRawCounts"
  num_lines: 1
deeptools/plotFingerprintOutQualityMetrics:
  contents: Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow
    Point	Synthetic Elbow Point
  num_lines: 1
deeptools/plotPCAData:
  contents: "#plotPCA --outFileNameData"
  num_lines: 1
deeptools/plotProfile:
  contents: bin labels
  num_lines: 1
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