All command line options
deepTools version: 1.5.7 (February 2014)
Here, you will find all the options available for the command line (almost all of them are also available in Galaxy, perhaps named slightly different).
You can always see all available command-line options via --help:
$ /deepTools/bin/bamCoverage --help
A typical deepTools command could look like this:
$ /deepTools/bin/bamCoverage --bam myAlignedReads.bam \
--outFileName myCoverageFile.bigWig \
--outFileFormat bigwig \
--fragmentLength 200 \
--ignoreDuplicates \
--scaleFactor 0.5
- output format of plots should be indicted by the file ending, e.g. MyPlot.pdf will return a pdf, MyPlot.png a png-file
- all tools that produce plots can also output the underlying data - this can be useful in case you don’t like the deepTools visualization as you can then use the data matrices produced by deepTools with your favorite plotting module, e.g. R or Excel
- numberOfProcessors
- region - in case you're testing whether a certain plot works and gives you the output you're hoping for, you can speed things up by focusing on a certain genome region, e.g. chr4 or chr2:100000200000
- ignoreDuplicates
- minMappingQuality
To tell a program to use a certain option (e.g. to ignore duplicate reads), you will have to give the option name preceded by two hyphens (e.g. --ignoreDuplicates). In the tables on this page, we try to list:
- the option name as recognized by the program
- the kind of value that is sometimes expected after the option name (see the annotated figure below)
- a verbose explanation of what the option actually does
The texts here are adjusted for readability, they might not match the help text that you see in the command line word by word.
- Mandatory parameters
- Optional parameters
- Additional output parameters
- Parameters for read processing
- Options for the heatmap
bamCorrelate can be run in two modes: bins and BED-file.
A typical command would like this:
$ /deepTools/bin/bamCorrelate BED-file \
--BED myRegionsOfInterest.bed \
--bamfiles myAlignedReads_Sample1.bam myAlignedReads_Sample2.bam \
--plotFile correlation_plot.png \
--corMethod pearson
For details on bamCorrelate, see the tool details.
| Command | Expected Input | Explanation |
|---|---|---|
| --bamfiles | FILENAMES | List of indexed BAM files separated by space (default: None) |
| --plotFile | FILENAME | File name to save the file containing the heatmap of the correlation. The file ending will be used to determine the image format, for example, if correlation.pdf is provided, the heatmap will be saved in pdf format. Available file format options are: .png, .emf, .eps, .pdf and .svg. (default: None) |
| --corMethod | {pearson, spearman} | Choose the method for the correlation calculation (default: None) |
| Command | Expected Input | Explanation | |:----:|:----:|:----| | --BED | FILENAME | If the comparison of read counts should be limited to certain regions, a BED file can be given. If this is the case, then the correlation is computed for the number of reads that overlap such regions. (default: None) |
| Command | Expected Input | Explanation | |:----:|:----:|:----| | --binSize | INT | Length in base pairs for a window used to sample the genome. (default: 10000) | | --numberOfSamples | INT | Number of random genome places to count reads for the correlation computation. (default: 1000000) |
| Command | Expected Input | Explanation |
|---|---|---|
| --includeZeros | If set, then zero counts that happen for all BAM files are included. The default behavior is to ignore those cases (default: False) | |
| --region | CHR:START:END | Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example: --region chr10 or --region chr10:456700:891000. (default: None) |
| --numberOfProcessors | INT | Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: max/2) |
| --verbose | Set to see processing messages. (default: False) |
| Command | Expected Input | Explanation |
|---|---|---|
| --fragmentLength | INT | Length of the average fragment size. Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. Warning the fragment length affects the normalization to 1x (see --normalizeUsingSequencingDepth). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragmentLength). NOTE: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the --fragmentLength. (default: 200) |
| --doNotExtendPairedEnds | If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the --fragmentLength. Default is to extend the reads if paired-end information is available. (default: False) | |
| --ignoreDuplicates | If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (default: False) | |
| --minMappingQuality | INT | If set, only reads that have a mapping quality score higher than --minMappingQuality are considered. (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --outFileCorMatrix | FILENAME | Output file name for the correlation matrix (tabulated text file). (default: None) |
| --outRawCounts | FILENAME | Output file name to save the bin counts (tabulated text file). (default: None) |
| --plotFileFormat | {png, emf, eps, pdf, svg} | If given, this option overrides the image format based on the ending given in --plotFile. (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --zMin | NUMBER | Minimum value for the heatmap intensities. If not specified the value is set automatically (default: None) |
| --zMax | NUMBER | Maximum value for the heatmap intensities. If not specified the value is set automatically (default: None) |
| --colorMap | {Spectral, summer, coolwarm, Set1, Set2, Set3, Dark2, hot, RdPu, YlGnBu, RdYlBu, gist_stern, cool, gray, GnBu, gist_ncar, gist_rainbow, CMRmap, bone, RdYlGn, spring, terrain, PuBu, spectral, gist_yarg, BuGn, bwr, cubehelix, YlOrRd, Greens, PRGn, gist_heat, Paired, hsv, Pastel2, Pastel1, BuPu, copper, OrRd, brg, gnuplot2, jet, gist_earth, Oranges, PiYG, YlGn, Accent, gist_gray, flag, BrBG, Reds, RdGy, PuRd, Blues, Greys, autumn, pink, binary, winter, gnuplot, RdBu, prism, YlOrBr, rainbow, seismic, Purples, ocean, PuOr, PuBuGn, afmhot} | Color map to use for the heatmap. For exemplary plots for all the color schemes, click here (default: Reds) |
| Command | Expected Input | Explanation |
|---|---|---|
| --bamfiles | FILENAME | List of sorted BAM files (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --plotFile | FILENAME | File name to save the image file containing a plot of the fingerprint, for example MyPlot.png (default: None) |
| --outRawCounts | FILENAME | Output file name to save the bin counts (default: None) |
| --plotFileFormat | {png, emf, eps, pdf, svg} | image format type. If given, this option overrides the image format based on the plotFile ending. (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --labels | LIST | List of labels to use in the output. If not given the file names will be used instead. Separate the labels by space. (default: None) |
| --binSize | INT | Length in base pairs for a window used to sample the genome. (default: 500) |
| --fragmentLength | INT | Length of the average fragment size. (default: 200) |
| --numberOfSamples | INT | Number of bins, sampled from the genome to compute the average number of reads. (default: 500000) |
| --skipZeros | If set, then zero counts that happen for all BAM files given are ignored. This will result in a reduced number of read counts than the the specified in --numberOfSamples (default: False) | |
| --region | CHR:START:END | Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) |
| --numberOfProcessors | INT | Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: max/2) |
| --verbose | Set to see processing messages. (default: False) |
| Command | Expected Input | Explanation |
|---|---|---|
| --doNotExtendPairedEnds | If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the --fragmentLength. Default is to extend the reads if paired end information is available. (default: False) | |
| --ignoreDuplicates | If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (default: False) | |
| --minMappingQuality | INT | If selected and accompanied by a number, only reads that have a mapping quality score higher than the given number are considered (e.g. --minMappingQuality 10)(default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --bamfile | FILENAME | Sorted BAM file. (default: None) |
| --effectiveGenomeSize | INT | The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. This value is needed to detect enriched regions that, if not discarded, can bias the results. If repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000. See Table 2 of this article or here for several effective genome sizes. (default: None) |
| --genome | FILENAME | Genome in 2bit format. Most genomes can be found here. Search for the .2bit ending. Otherwise, FASTA files can be converted to 2bit using the UCSC programm called faToTwoBit available for different plattforms at http://hgdownload.cse.ucsc.edu/admin/exe/ (default: None) |
| --fragmentLength | INT | Fragment length used for the sequencing. If paired-end reads are used the fragment length is computed from the BAM file (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --GCbiasFrequenciesFile | FILE NAME | Indicate a file name where the observed and expected read frequencies per GC content can be saved in. This file will be needed to run the correctGCBias tool. This is a text file. (default: None) |
| --plotFileFormat | {png, emf, eps, pdf, svg} | image format type. If given, this option overrides the image format based on the plotFile ending. (default: None) |
| --biasPlot | FILENAME | found on the sample will be saved. (default: None) |
| --regionSize | INT | To plot the reads per GC over a region, the size of the region is required. By default, the region size is set to 300 bp, which is close to the standard fragment size for Illumina machines. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read (default: 300) |
| Command | Expected Input | Explanation |
|---|---|---|
| --sampleSize | INT | Define how many regions in the genome should be sampled for the calculation of the read distributions. (default: 50000000) |
| --filterOut | FILENAME | In some cases, it will make sense to exclude certain regions from the calculation of the read distributions. To tell computeGCbias where not to sample, please provide the path to a BED file of regions that should be excluded. See the entry on computeGCbias for further details. (default: None) |
| --extraSampling | FILENAME | BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome. This could be regions of extreme GC contents. (default: None) |
| --version | show program's version number and exit | |
| --region | CHR:START:END | Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) |
| --numberOfProcessors | INT | Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: max/2) |
| --verbose | Set to see processing messages. (default: False) |
| Command | Expected Input | Explanation |
|---|---|---|
| --bam | FILENAME | BAM file to process (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --outFileName | FILENAME | Output file name. (default: None) |
| --outFileFormat | {bigwig,bedgraph} | Output file type. |
| Command | Expected Input | Explanation |
|---|---|---|
| --bamIndex | FILENAME | Index for the BAM file. Default is to consider the path of the BAM file adding the .bai suffix. (default: None) |
| --scaleFactor | NUMBER | Indicate a number that you would like to use as a fixed scaling factor instead of the scaling factor calculated by the --normalizeUsingSequencingDepth option. (default: 1) |
| --normalizeTo1x | NUMBER | Report read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC)). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. To use this option, the effective genome size has to be indicated after the command**. The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Common values are: mouse/mm9: 2150570000, human/hg19:2451960000, D.melanogaster/dm3:121400000 and C.elegans/ce10:93260000. See Table 2 of this article or here for several effective genome sizes. (default: None) |
| --normalizeUsingRPKM | Use Reads Per Kilobase per Million reads to normalize the number of reads per bin. The formula is: RPKM (per bin) = number of reads per bin / ( number of mapped reads ( in millions) * bin length (kb) ) (default: False) | |
| --ignoreForNormalization | LIST | A list of chromosome names separated by comma and limited by quotes, containing those chromosomes that want to be excluded for computing the normalization. For example, --ignoreForNormalization "chrX, chrM" (default: None) |
| --binSize | INT | Size of the bins in bp for the output of the bigWig/bedGraph file. (default: 50) |
| --region | CHR:START:END | Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) |
| --numberOfProcessors | INT | Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: max/2) |
| --verbose | Set to see processing messages. (default: False) |
| Command | Expected Input | Explanation |
|---|---|---|
| --fragmentLength | INT | Length of the average fragment size. Reads will be extended to match this length unless they are paired- end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. Warning the fragment length affects the normalization to 1x (see --normalizeUsingSequencingDepth). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragmentLength). NOTE: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the --fragmentLength. (default: 200) |
| --smoothLength | INT | The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the --binSize is set to 20 bp and the --smoothLength is set to 60 bp, then, for each binSize the average of it and its left and right neighbors is considered. Any value smaller than the --binSize will be ignored and no smoothing will be applied. (default: None) |
| --doNotExtendPairedEnds | If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the --fragmentLength. Default is to extend the reads if paired end information is available. (default: False) | |
| --ignoreDuplicates | If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (default: False) | |
| --minMappingQuality | INT | If set, only reads that have a mapping quality score higher than --minMappingQuality are considered. (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --bamfile1 | FILENAME | Sorted BAM file 1. Usually the BAM file for the treatment. (default: None) |
| --bamfile2 | FILENAME | Sorted BAM file 2. Usually the BAM file for the control. (default: None) |
| Command | Expected Input | Explanation |
|---|---|---|
| --outFileName | FILENAME | Output file name. (default: None) |
| --outFileFormat | {bigwig, bedgraph} | Output file type. |
| Command | Expected Input | Explanation |
|---|---|---|
| --bamIndex1 | FILENAME | Index for the BAM file 1. Default is to consider the path of the BAM file and adding the .bai suffix. (default: None) |
| --bamIndex2 | FILENAME | Index for the BAM file 1. Default is to consider the path of the BAM file adding the .bai suffix. (default: None) |
| --scaleFactorsMethod | {readCount,SES} | Method for scaling the samples. SES is only recommended when signal and noise are well separated which can be seen in the bamFingerprint plot. (default: readCount) |
| --sampleLength | INT | Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two BAM files (default: 1000) |
| --scaleFactors | NUMBER:NUMBER | Set this parameter to avoid the computation of scaleFactors. The format is scaleFactor1:scaleFactor2. For example 0.7:1 to scale the first BAM file by 0.7 while not scaling the second BAM file (default: None) |
| --pseudocount | NUMBER | small number to avoid log2(x/0) (default: 1) |
| --ratio | {log2, ratio, subtract, add, reciprocal_ratio} | The default is to output the log2ratio between the two samples. The reciprocal ratio returns the the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes. (default: log2) |
| --normalizeUsingRPKM | only to be set when --ratio subtract is selected | If you would like to get the difference between 2 BAM files (and hence set --ratio subtract), the final score will be normalized for sequencing depth so that the file can be compared to other samples from different sequencing runs, too. The default normalization method is R Per Kilobase per Million reads. The formula is: RPKM (per bin) = #reads per bin / ( # of mapped reads (millions) * bin length (KB)). Example usage: --normalizeUsingRPKM |
| --normalizeTo1x | NUMBER (only when --ratio subtract) | The difference will be reported normalized for sequencing depth. The default method is RPKM (see above). If you would like to report the normalized coverage to 1x sequencing depth, set this option and indicate the effective genome size. Sequencing depth is defined as the total number of mapped reads*fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mouse/mm9: 2150570000, human/hg19:2451960000, D.melanogaster/dm3:121400000 and C.elegans/ce10:93260000. Example usage: --normalizeTo1x 2150570000 |
| --numberOfSamples | INT | How many times the genome should be sampled to compute the scaling factors (default: 100000) |
| --missingDataAsZero | {yes,no} | This parameter determines if missing data should be treated as zeros. If set to "no", missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads. (default: yes) |
| --ignoreForNormalization | LIST | A list of chromosome names separated by comma and limited by quotes, containing those chromosomes that you want to be excluded for computing the normalization. For example, --ignoreForNormalization "chrX, chrM" (default: None) |
| --binSize | INT | Size of the bins in bp for the output of the bigWig/bedGraph file. (default: 50) |
| --region | CHR:START:END | Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) |
| --numberOfProcessors | INT | Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: max/2) |
| --verbose | Set to see processing messages. |
| Command | Expected Input | Explanation |
|---|---|---|
| --fragmentLength | INT | Length of the average fragment size. Reads will be extended to match this length unless they are paired- end, in which case they will be extended to match the fragment length. If this value is set to the [read][] length or smaller, the read will not be extended. Warning the fragment length affects the normalization to 1x (see --normalizeUsingSequencingDepth). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragmentLength). NOTE: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the --fragmentLength. (default: 200) |
| --smoothLength | INT | The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the --binSize is set to 20 bp and the --smoothLength is set to 60 bp, then, for each binSize the average of it and its left and right neighbors is considered. Any value smaller than the --binSize will be ignored and no smoothing will be applied. (default: None) |
| --doNotExtendPairedEnds | If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the --fragmentLength. Default is to extend the reads if paired end information is available. (default: False) | |
| --ignoreDuplicates | If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (default: False) | |
| --minMappingQuality | INT | If selected and accompanied by a number, only reads that have a mapping quality score higher than the given number are considered (e.g. --minMappingQuality 10)(default: None) |
computeMatrix can be run in two modes: scale-regions and reference-point.
For details on the differences between the two modes, please check the tool details: computeMatrix
| Command | Expected Input | Explanation |
|---|---|---|
| --regionsFileName | FILENAME | File should and contain the regions to plot in BED or GFF format. (default: None) |
| --scoreFileName | FILENAME | bigWig file with the scores to be visualized. BigWig files can be obtained by using the bamCoverage or bamCompare tools. |
| Command | Expected Input | Explanation | |:----:|:----:|:----| | --regionBodyLength | INTEGER | Distance in bp to which all regions are going to be fitted. (default: 1000) | | --startLabel | NAME | Label shown in the plot for the start of the region. Default is region start site, but this could be changed to anything, e.g. "peak start". (default: TSS) | | --endLabel | NAME | Label shown in the plot for the region end. Default is the region end site. (default: TES) |
| Command | Expected Input | Explanation | |:----:|:----:|:----| | --referencePoint | {TSS;TES;center} | The reference point for the plotting could be either the region start (TSS), the region end (TES) or the center of the region. (default: TSS) | | --nanAfterEnd | | If set, any values after the region end are discarded. This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the start of the region. (default: False) |
| Command | Expected Input | Explanation |
|---|---|---|
| --beforeRegionStartLength | INTEGER | Distance upstream of the reference-point selected. (default: 500) |
| --afterRegionStartLength | INTEGER | Distance downstream of the reference-point selected. (default: 1500) |
| --binSize | INTEGER | Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length. (default: 10) |
| --sortRegions | {descend,ascend,no} | Whether the output file should present the regions sorted. The default is to sort in descending order based on the mean value per region. (default: no) |
| --sortUsing | {mean,median,max,min,sum,region_length} | Indicate which method should be used for sorting. The value is computed for each row. (default: mean) |
| --averageTypeBins | {mean,median,min,max,std,sum} | Define the type of statistic that should be used over the bin size range. The options are: "mean", "median", "min", "max", "sum" and "std". The default is "mean". (default: mean) should be indicated as zeros. Default is to ignore such cases which will be depicted as black areas in the heatmap. (see --missingDataColor argument of the heatmapper for additional options). (default: False) |
| --skipZeros | Whether regions with only scores of zero should be included or not. Default is to include them. (default: False) | |
| --minThreshold | NUMBER | Numeric value. Any region containing a value that is equal or less than this numeric value will be skipped. This is useful to skip, for example, genes where the read count is zero for any of the bins. This could be the result of unmappable areas and can bias the overall results. (default: None) |
| --maxThreshold | NUMBER | Numeric value. Any region containing a value that is equal or higher that this numeric value will be skipped. The maxThreshold is useful to skip those few regions with very high read counts (e.g. major satellites) that may bias the average values. (default: None) |
| --quiet | Set to remove any warning or processing messages. (default: False) | |
| --scale | NUMBER | If set, all values are multiplied by this number. (default: 1) |
| --numberOfProcessors | INTEGER | Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: max/2) |
| Command | Expected Input | Explanation |
|---|---|---|
| --outFileName | FILENAME | File name to save the gzipped matrix file which will be used by heatmapper and profiler. (default: None) |
| --outFileNameData | OUTFILENAMEDATA | Name to save the averages per matrix column into a text file. This corresponds to the underlying data used to plot a summary profile. Example: myProfile.tab (default: None) |
| --outFileNameMatrix | FILE | If this option is given, then the matrix of values underlying the heatmap will be saved using the indicated name, e.g. IndividualValues.tab.This matrix can easily be loaded into R or other programs. (default: None) |
| --outFileSortedRegions | BED | File name in which the regions are saved after skiping zeros or min/max threshold values. The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap. Example: Heatmap1sortedRegions.bed (default: None) |
[read]: https://github.com/fidelram/deepTools/wiki/Glossary#terminology "the DNA piece that was actually sequenced ("read") by the sequencing machine (usually between 30 to 100 bp long, depending on the read-length of the sequencing protocol)" [input]: https://github.com/fidelram/deepTools/wiki/Glossary#terminology "confusing, albeit commonly used name for the 'no-antibody' control sample for ChIP experiments"