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Performs peak calling for ChIP-Seq data.

Parameters in GUI

ParameterDescriptionDefault value
Output directoryDirectory to save MACS output files. 
NameThe name string of the experiment. MACS will use this string NAME to create output files like 'NAME_peaks.xls', 'NAME_negative_peaks.xls', 'NAME_peaks.bed', 'NAME_summits.bed', 'NAME_model.r' and so on. So please avoid any confliction between these filenames and your existing files (--name). 
Wiggle outputIf this flag is on, MACS will store the fragment pileup in wiggle format for the whole genome data instead of for every chromosomes (--wig) (--single-profile).hg19
Wiggle spaceBy default, the resolution for saving wiggle files is 10 bps,i.e., MACS will save the raw tag count every 10 bps. You can change it along with '--wig' option (--space).3000
Genome size (Mbp)Homo sapience - 2700 Mbp
Mus musculus - 1870 Mbp
Caenorhabditis elegans - 90 Mbp
Drosophila melanogaster - 120 Mbp
It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromosomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size (--gsize).
P-valueP-value cutoff. Default is 0.00001, for looser results, try 0.001 instead (--pvalue).3000
Tag size (optional)Length of reads. Determined from first 10 reads if not specified (input 0) (--tsize).5000
Keep duplicatesIt controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The default auto option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the all option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location (--keep-dup).3000
Use modelWhether or not to use MACS paired peaks model (--nomodel). 
Model foldSelect the regions within MFOLD range of high-confidence enrichment ratio against. Model fold is available when Use model is true, which is the foldchange to chose paired peaks to build paired peaks model. Users need to set a lower(smaller) and upper(larger) number for fold change so that MACS will only use the peaks within these foldchange range to build model (--mfold). 
Shift sizeAn arbitrary shift value used as a half of the fragment size when model is not built. Shift size is available when Use model is false, which will represent the HALF of the fragment size of your sample. If your sonication and size selection size is 300 bps, after you trim out nearly 100 bps adapters, the fragment size is about 200 bps, so you can specify 100 here (--shiftsize). 
Band widthThe band width which is used to scan the genome for model building. You can set this parameter as the sonication fragment size expected from wet experiment. Used only while building the shifting model (--bw). 
Use lambdaWhether to use local lambda model which can use the local bias at peak regions to throw out false positives (--nolambda). 
Small nearby regionThe small nearby region in basepairs to calculate dynamic lambda. This is used to capture the bias near the peak summit region. Invalid if there is no control data (--slocal). 
Large nearby regionThe large nearby region in basepairs to calculate dynamic lambda. This is used to capture the surround bias (--llocal). 
Auto bimodalWhether turn on the auto pair model process.If set, when MACS failed to build paired model, it will use the nomodelsettings, the “Shift size” parameter to shift and extend each tags (--on-auto). 
Scale to largeWhen set, scale the small sample up to the bigger sample.By default, the bigger dataset will be scaled down towards the smaller dataset,which will lead to smaller p/qvalues and more specific results.Keep in mind that scaling down will bring down background noise more (--to-large). 

Parameters in Workflow File

Type: macs-id

ParameterParameter in the GUIType
output-dirOutput directory


wiggle-outputWiggle outputboolean
wiggle-spaceWiggle spacenumeric
genome-sizeGenome size (Mbp)numeric
tag-sizeTag size (optional)numeric
keep-duplicatesKeep duplicatesstring
use-modelUse modelboolean
model-foldModel foldstring
shift-sizeShift sizenumeric
band-widthBand widthnumeric
use-lambdaUse lambdaboolean
small-nearbySmall nearby regionnumeric
large-nearbyLarge nearby regionnumeric
auto_bimodalAuto bimodalboolean
scale_largeScale to largeboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: MACS data

Name in Workflow File: in-data


Slot In GUISlot in Workflow FileType
Treatment features_treatment-annann-table-list
Control featurescontrol-annann-table-list

And 1 output port:

Name in GUI: MACS output data

Name in Workflow File: out-data


Slot In GUISlot in Workflow FileType
Peak regionspeak-regionsann-table-list
Peak summitspeak-summitsann-table-list
Treatment fragments pileupwiggle-treatstring



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