deepTools 2.0

Major changes

• computeMatrix now accepts multiple bigwig files that can later be plotted together as heatmaps
  one after the other or as multiple lines in the same plot. See the documentation of plotHeatmap
  and plotProfile for examples.
• computeMatrix also now accepts multiple input BED files. Each is treated as a group within a sample
  and is plotted independently.
• Added new analysis tool :doc:tools/plotPCA to visualize the results of multiBamCoverage
  or tools/multiBigwigSummary using principal component analysis.
• Added new quality control tool tools/plotCoverage to plot the coverage over base pairs for multiple samples
• Dramatically improved the speed of bigwig related tools (multiBigwigSummary and computeMatrix)
  by using the new pyBigWig module.
• Added support for split reads (most commonly found in RNA-seq data).
• Added new option --MNase in bamCoverage that computes reads coverage only considering two
  base pairs at the center of the fragment.
• Added --samFlagInclude and --samFlagExclude parameters. This is useful to for example
  only include forward reads (or only reverse reads) in an analysis.
• Plotting of correlations (from multiBamCoverage or multiBigwigSummary) is now
  separated from the computation of the underlying data. A new tool, plotCorrelation was added. This tool
  can plot correlations as heatmaps or as scatter plots and includes options to adjust a large array of visual features.
• Added hierarchical clustering, besides k-means to plotProfile and plotHeatmap
• Correlation coefficients can now be computed even if the data contains NaNs.
• The documentation was migrated to http://deeptools.readthedocs.org
• deepTools modules can now be used by other python programs. The :ref:api is now part of the documentation.
• In this new release, most of the core code was rewriting to facilitate API usage and for optimization.

Minor changes

• --missingDataAsZero was renamed to --skipNonCoveredRegions for clarity in :doc:tools/bamCoverage
  and :doc:tools/bamCompare.
• Read extension was made optional and removed the need to specify a default fragment length for most of the tools.
  and --fragmentLentgh parameters were replaced by the new optional parameter --extendReads.
• Renamed:
  • heatmapper to :doc:tools/plotHeatmap
  • profiler to :doc:tools/plotProfile
  • bamCorrelate to multiBamCoverage
  • bigwigCorrelate to multiBigwigSummary
  • bamFingerprint to :plotFingerprint.
• Improved plotting features for plotProfile when using as plot type: 'overlapped_lines' and 'heatmap'
• Resolved an error introduced by numpy version 1.10 in :doc:tools/computeMatrix
• Fixed problem with bed intervals in multiBigwigSummary and multiBamCoverage and a
  user specified region that returned wrongly labeled raw counts.
• computeMatrix can now read files with DOS newline characters.
• Added option --skipChromosomes to :doc:tools/multiBigwigSummary, for example to skip all
  'random' chromosomes. multiBigwigSummary now also considers chromosomes as identical
  when the names between samples differ by 'chr' prefix 'chr'. E.g. chr1 vs. 1
• For :doc:tools/bamCoverage and bamCompare, behaviour of scaleFactor was updated such that now,
  if given in combination with the normalization options (normalize to 1x or normalize using RPKM) the given scaleFactor
  will multiply the scale factor computed for the normalization methods.
• Fixed problem with wrongly labeled proper pairs in a bam file. deepTools adds further checks to
  determine if a read pair is a proper pair.
• Added titles to QC plots,

Added support to BED files with DOS end of lines

1.5.13

increased version number to 1.5.13

Fixed issue with sorting bedgraph files

Merge pull request #117 from fidelram/agg_plotting

Use Agg as default plotting backend.

1.5.11

Fixed rare problem with bigwig files that blocked the program execution.

Enhancements of galaxy wrappers

1.5.9.1

Added a fix to bamCorrelate under BED-file mode which was wrongly reducing the size of the BED region to 1.

1.5.9

• Fixed problem with pseudocounts. The original implementation was scaling pseudocounts twice, which resulted in unexpected results for regions with zero reads.
• The tools bigWigCorrelate and bamPEFragmentSize where added to galaxy.
• Added parameter missingDataAsZero to bamCoverage. The default behaviour is unchanged.
• Improved error reporting of bamCorrelate when few bins are computed.

Overall improvements

This release improves the command line installation of deepTools, warning the user when some dependencies are not found.

In regard to the heatmapper we fixed a problem with overlapping labels and overlapping cluster/group names.

Also we changed the default behaviour of computeMatrix to be verbose by default. This is to warn the user of potential problems with the BED regions usually related to duplications and regions with no signal. We also added automatic mapping of chromosome names with and without chr.

For bamCoverage we changed the behavior: now, genome regions without read coverage show a zero. Before, such regions where not part of the bedgraph/bigwig output.

Improved installation, addition of --version to the tools

New in this release:

• Improved installation, now the installation checks if the UCSC dependencies are installed, if not, a message is shown indicating where to get missing programs and pointing the user to the configuration file to edit.
• when running bamCoverage or bamCompare, the system now checks if bedGraphTobigWig is installed, if not, a message is issued and the tools return a bedGraph file instead.
• We added the --version argument to our tools
• A number of bug fixes.

Stable release

For this release we mostly changed the behavior of the heatmapper. Before, the creation of the underlying matrix (a slow process) and the visualization were done together. However, most of the time the visualization required adjustments, for example to try different color combinations. Because of this we separated the creation of the matrix and the plotting of the data. Moreover we added a tool only for plotting a profile. This was also part of the heatmapper before but the number of options was growing too much and we decided it was better to divide the functionality.

Also, we changed the original names of several functions to better reflect their functionality.