Tools to process and analyze deep sequencing data.
--plotNumbers not working in plotCorrelation. This was issue #838.plotCoverage now has a --BED option, to restrict plots and output to apply to a specific set of regions given by a BED or GTF file or files (issue #829).plotCoverage now has a --DepthSummary option, which produces a summary similar to GATK's DepthOfCoverage (issue #828).plotCoverage is now able to compute coverage metrics for arbitrary coverage thresholds using multiples of the -ct option (e.g., -ct 0 -ct 10 -ct 20 -ct 30).estimateReadFiltering where the estimated number of filtered reads was typically too low.bamCoverage if RPGC normalization is requested but no effective genome size is provided (issue #815).--labels option in most tools (issue #738)std plot type to plotProfile in Galaxy (issue #782)bamCompare now has a --skipZeroOverZero option to allow skipping bins where both input files lack coverage (issue #785)bamCompare and bigwigCompare can now take two pseudocounts, in case you want a different value for the numerator and the denominator (issue #784)multiBamSummary now has a --scaleFactors option, which computes scale factors in the same manner as DESeq2 to a file. Note that the produced scaling factors are meant to be used with bamCoverage. If you want to use them directly in DESeq2 (or a similar package) you will need to invert them (take 1/scale factor). (issue #800)--legendLocation option in the Galaxy wrappers for plotProfile and plotHeatmap--markers option to plotPCA, courtesy of @sklasfeld.computeMatrixOperations rbind now properly supports multiple region groups (issue #742)--xRange and --yRange with plotCorrelation (issue #709)--outFileNameData option in plotProfile when computeMatrix reference-point --referencePoint center was used. This caused an error previously. (issue #727)--scaleFactor option in bamCoverage are no longer mutually exclusive.--centerReads option in bamCoverage is now compatible with --Offset (previously --centerReads was silently ignored if --Offset was specified). (issue #693)bamCoverage and bamCompare now have an --exactScaling option. Instead of using a random sample of alignment to compute the scaling factor, this causes all reads in the file to be used. This is significantly slower, but helpful in situations where reads that should be excluded clump together on the genome (i.e., when sampling based on location is likely to be inaccurate).plotCorrelation --whatToPlot scatterplot now has --xRange and --yRange options rather than just --maxRange. (issue #709)computeMatrixOperations can now be used to change sample and group names.computeMatrixOperations can now filter rows by minimum and/or maximum value.--maxThreshold and --minThreshold are now more consistently honoured. (#702)--normalizeUsing RPGC with bamCompare will now result in a fatal error, rather than a simple warning and the settings being changed under the hood. (#718)--normalizeUsing to anything other than None will result in an error unless --scaleFactorsMethod None is also used. This is to prevent people from accidentally getting unintended normalization.computeMatrix now has a --verbose option. Setting this will drastically increase the verbosity of the messages sent to the screen. Only do this for debugging. --quiet will disable this completely (as well as all other messages printed to screen).--sortUsing region_length in plotHeatmap. This now works properly for --referencePoint center and --referencePoint TES, where in the latter case the dashed line is drawn at the region start. The documentation has been updated to mention this. (issue #671)computeMatrix reference-point is now respected by plotHeatmap and plotProfile. So if you used computeMatrix reference-point --referencePointLabel center then 'center' will now appear as the tick label in your heatmaps and profiles automatically. (issues #606 and #683). in the chromosome name in the Galaxy wrappers (issue #692)--perGroup option in plotProfile and plotHeatmap when multiple groups were being used. In version 3.0.0, this would typically cause an error and deepTools to crash. (issue #673)