# The tools¶

Note

With the release of deepTools 2.0, we renamed a couple of tools:

For more, see Changes in deepTools2.0.

tool type input files main output file(s) application
multiBamSummary data integration 2 or more BAM interval-based table of values perform cross-sample analyses of read counts –> plotCorrelation, plotPCA
multiBigwigSummary data integration 2 or more bigWig interval-based table of values perform cross-sample analyses of genome-wide scores –> plotCorrelation, plotPCA
plotCorrelation visualization bam/multiBigwigSummary output clustered heatmap visualize the Pearson/Spearman correlation
plotPCA visualization bam/multiBigwigSummary output 2 PCA plots visualize the principal component analysis
plotFingerprint QC 2 BAM 1 diagnostic plot assess enrichment strength of a ChIP sample
computeGCBias QC 1 BAM 2 diagnostic plots calculate the exp. and obs. GC distribution of reads
correctGCBias QC 1 BAM, output from computeGCbias 1 GC-corrected BAM obtain a BAM file with reads distributed according to the genome’s GC content
bamCoverage normalization BAM bedGraph or bigWig obtain the normalized read coverage of a single BAM file
bamCompare normalization 2 BAM bedGraph or bigWig normalize 2 files to each other (e.g. log2ratio, difference)
computeMatrix data integration 1 or more bigWig, 1 or more BED zipped file for plotHeatmap or plotProfile compute the values needed for heatmaps and summary plots
estimateReadFiltering information 1 or more BAM files table of values estimate the number of reads filtered from a BAM file or files
alignmentSieve QC 1 BAM file 1 filtered BAM or BEDPE file filters a BAM file based on one or more criteria
plotHeatmap visualization computeMatrix output heatmap of read coverages visualize the read coverages for genomic regions
plotProfile visualization computeMatrix output summary plot (“meta-profile”) visualize the average read coverages over a group of genomic regions
plotCoverage visualization 1 or more BAM 2 diagnostic plots visualize the average read coverages over sampled genomic positions
bamPEFragmentSize information 1 BAM text with paired-end fragment length obtain the average fragment length from paired ends
plotEnrichment visualization 1 or more BAM and 1 or more BED/GTF A diagnostic plot plots the fraction of alignments overlapping the given features
computeMatrixOperations miscellaneous 1 or more BAM and 1 or more BED/GTF A diagnostic plot plots the fraction of alignments overlapping the given features

## General principles¶

A typical deepTools command could look like this:

$bamCoverage --bam myAlignedReads.bam \ --outFileName myCoverageFile.bigWig \ --outFileFormat bigwig \ --fragmentLength 200 \ --ignoreDuplicates \ --scaleFactor 0.5  You can always see all available command-line options via –help: $ bamCoverage --help

• Output format of plots should be indicated by the file ending, e.g. MyPlot.pdf will return a pdf file, MyPlot.png a png-file
• All tools that produce plots can also output the underlying data - this can be useful in cases where you don’t like the deepTools visualization, as you can then use the data matrices produced by deepTools with your favorite plotting tool, such as R
• The vast majority of command line options are also available in Galaxy (in a few cases with minor changes to their naming).

### Parameters to decrease the run time¶

• numberOfProcessors - Number of processors to be used
For example, setting --numberOfProcessors 10 will split up the
workload internally into 10 chunks, which will be processed in parallel.
• region - Process only a single genomic region.
This is particularly useful when you’re still trying to figure out the best parameter setting. You can focus on a certain genomic region by setting, e.g., --region chr2 or --region chr2:100000-200000

These parameters are optional and available throughout almost all deepTools.

### Filtering BAMs while processing¶

Several deepTools modules allow for efficient processing of BAM files, e.g. bamCoverage and bamCompare. We offer several ways to filter those BAM files on the fly so that you don’t need to pre-process them using other tools such as samtools

• ignoreDuplicates
Reads with the same orientation and start position will be considered only once. If reads are paired, the mate is also evaluated
• minMappingQuality
Only reads with a mapping quality score of at least this are considered
• samFlagInclude
Include reads based on the SAM flag, e.g. --samFlagInclude 64 gets reads that are first in a pair. For translating SAM flags into English, go to: https://broadinstitute.github.io/picard/explain-flags.html
• samFlagExclude
Exclude reads based on the SAM flags - see previous explanation.

These parameters are optional and available throughout deepTools.

Note

In version 2.3 we introduced a sampling method to correct the effect of filtering when normalizing using bamCoverage or bamCompare. For previous versions, if you know that your files will be strongly affected by the filtering of duplicates or reads of low quality then consider removing those reads before using bamCoverage or bamCompare, as the filtering by deepTools is done after the scaling factors are calculated!