The following is a list of the available features and options (Hence: The parameters enclosed between square brackets are optional).
| -i input_file |
Input data file path (The standard 6-column BED, BAM and SMA file formats are accepted). |
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| -o output_label |
Used to label the output directory and file names. |
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| [-control control_file.bed] |
Background data file path (The standard 6-column BED, BAM and SMA file formats are accepted). |
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| [-chr chromosome] |
Forces PFMS to only process the specified chromosome instead of handling all the chromosomes of the input file. |
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| [-store_results] |
Keeps the original files generated by the peak-finders (plus results of the spitted chromosomes when -all chr is used) |
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| [-min_rank number] |
A peak is significant if it’s detected by given ¡number¿ peak-finders (the default is number of selected peak finders/2) (it should be in range of the quantity of the selected peak finders). |
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| [-bed | -sam | -bam] |
Specifies the input file format (bed is the default value). The read and control files have to have the same format as specified here. |
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| [-wig] |
Gives the detected peaks in WIG format while the default is BED. (please note this feature can only be used with MACS, CisGenome, FindPeaks and HPeak). For this option only -average and -quantile normalization types can be used. |
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| [-output percentage number] |
The percentage of the identified peaks to be obtained (default is 100), to be used only with -wig option. |
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| [ -voting | -minFN | -minFP] |
Uses the specified peak selection mechanism (the default value is voting), not to be used with -wig. |
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| [ -quantile number | -normal [-normal_shift number]| -rank | -average | -top_rank] |
Specifies a normalization method for normalizing the peak-scores (the default method is quantile with value of 75). |
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| [-parallel] |
Forces PFMS to execute the peak-finders in parallel (it is the default if more than two processors are available). |
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| [-sequential] |
Forces PFMS to execute the peak-finders Sequentially (it is the default mode when fewer than two processors are available or the Python 2.6 or higher is not available) |
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| [-max_cpu_use number] |
Sets the maximum number of processors to be used by PFMS (default is 6) |
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| [-min_cpu number] |
PFMS is running in parallel mode if minimum number of processors (CPU) was available on the system (default is 2) |
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| -min_size number] |
Minimum file size (in KB) of a peak-finder result in order to be included in the comparison (default is 1KB) |
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| [-all_chr] |
Executes PFMS for each chromosome in a given dataset and combines the results (this is the default value) |
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| [-cisgenome] |
Detects the binding sites using CisGenome |
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| [-macs] |
Detects the binding sites using MACS |
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| [-findpeaks] |
Detects the binding sites using Findpeaks |
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| [-hpeak] |
Detects the binding sites using HPeak [18] (can be used with no presence of control data) |
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| [-erange] |
Detects the binding sites using Erange [19] (can be used only with BED comparison approach) |
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| [-sissr] |
Detects the binding sites using SISSRs [17] (can be used with BED comparison approach) |
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| [-seqsite] |
Detects the binding sites using SeqSite [20] (can be used only with BED comparison approach) |
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| [-help] |
Prints a usage message with a list of the available options. |
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Initially, PFMS uses the default parameters of each of the selected peak-finders. Meanwhile, All the selected peak-finders can be customized through altering PFMS's configuration file.
Assume, a ChIP-seq data file is named 'Treat.bed' and a control data is named 'Input.bed', both are located under the current working directory. The experiment goal is to find all the TFBSs in chromosome four that are identified by, at least, four peak finders out of six with using BED comparison approach and label the results with 'FoxA1 peaks'. In addition, keep results of all the peak finders.
