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MACS

Finds peaks from aligned short-reads. This component is a wrapper for a command line program MACS. NOTE: only works with 1.4.x version of MACS.

Version 1.1
Bundle microarray
Categories Short-read Sequencing
Specialties generic
Authors Erkka Valo (erkka.valo@helsinki.fi), Maria Yli-Heikkila (maria.yli-heikkila@helsinki.fi)
Issue tracker View/Report issues
Requires MACS 1.4.1 ; R
Source files component.xml MACS.java
Usage Example with default values

Type parameters (generics)

Inputs

Name Type Mandatory Description
treatment T1 (generic) Mandatory File containing aligned short-reads. These will be used as the treatment set for MACS.
control T1 (generic) Mandatory File containing aligned short-reads. These will be used as the control set for MACS.

Outputs

Name Type Description
peaks CSV Called peaks.
negativePeaks CSV Negative peaks. Negative peaks are called by swapping the treatment and control sample
report Latex A Latex report of the model fitting.
wiggle WiggleFolder A folder containg wiggle files for every chromosome.
bedGraph BinaryFolder A folder containg bedGraph files of aligned tags after shifting.

Parameters

Name Type Default Description
bw int 165 Band width. This value is used while building the shifting model.
fdrThreshold float 1 Peaks with FDR-value above threshold (exclusive) will be filtered out of the results.
fileFormat string "AUTO" Format of tag file, "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDMULTIPET", "SAM", "BAM" or "BOWTIE". With the default value "AUTO" MACS decides which format the file is.
gSize float 2700000000 Effective genome size.
keepDup string "auto" Controls how MACS handles duplicate tags at the same location (same coordinates and strand). With the default 'auto' option an upper limit for the maximum number of tags at the same location is calculated based on binomal distribution using 1e-5 as pvalue cutoff and the 'all' option keeps every tag. If an integer is given, at most this number of tags will be kept at the same location.
mFold string "10,30" A lower and upper limit separated by a comma. The regions having enrichment ratio between the lower and upper limit against the background are used to build the model.
macsCommand string "macs" MACS executable.
noModel boolean false If true, MACS does not build paired-peak model to determine the shift size of the tags. The value of parameter shitfSize is used for shifting the tags.
outputBedGraph boolean false Set to produce shifted raw tag count at every bp as a BedGraph file. WARNING: this process is time/space consuming!! This overrides useWiggle if both are set.
pValue float 1e-5 P-value cutoff for peak detection.
pythonDir string "" MACS python library installation directory. Check MACS installation instructions for more information. Value of this parameter, if given, will be added to the enviroment variable PYTHONPATH.
sectionTitle string "" Title for a new latex section. If non is given, a new section is not created.
sectionType string "section" Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty.
shiftSize int 100 While noModel is true or when MACS fails to build paired-peak model, MACS uses this parameter to shift tags to their midpoint.
tSize int 30 Tag size i.e. the length of the short-reads given as input to the component.
uniqueIDPrefix string "" If given, generate an unique ID for each peak with the prefix.
useWiggle boolean false Set to produce shifted raw tag count at every bp as an wiggle file. WARNING: this process is time/space consuming!!

Test cases

Test case Parameters IN
treatment
IN
control
OUT
peaks
OUT
negativePeaks
OUT
report
OUT
wiggle
OUT
bedGraph
case1 properties treatment control peaks negativePeaks report wiggle (missing)

pValue=0.1,
shiftSize=65,
gSize=110000

case2 properties treatment control peaks negativePeaks report (missing) (missing)

macsCommand=macs14,
pythonDir=/opt/macs/lib/python2.5/site-packages,
mFold=1,20,
fileFormat=BED,
gSize=110000,
pValue=0.01,
useWiggle=true,
fdrThreshold=0.01,
sectionTitle=Results


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