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Output

MSPC persists the results of each execution to a separate folder. Users can specify the output directory via the optional argument -o | --output; if not specified, MSPC creates an output directory with the following naming scheme. 

session_[DATE]_[TIME]

// For example:
session_20191126_222131330

Each output folder contains the following information:

A log file that contains the execution log; Consensus peaks in standard BED and MSPC format; One folder per each replicates contains BED files containing stringent, weak, background, confirmed, discarded, true-positive, and false-positive peaks. You may refer to the Sets page for a detailed description of each category.

An MSPC generated output for two replicates rep1 and rep2 is as the following: 

.
└── session_20210309_131747501
    ├── ConsensusPeaks.bed
    ├── ConsensusPeaks_mspc_peaks.txt
    ├── EventsLog_20210309_1317475050929.txt
    ├── rep1
    │   ├── Background.bed
    │   ├── Background_mspc_peaks.txt
    │   ├── Confirmed.bed
    │   ├── Confirmed_mspc_peaks.txt
    │   ├── Discarded.bed
    │   ├── Discarded_mspc_peaks.txt
    │   ├── FalsePositive.bed
    │   ├── FalsePositive_mspc_peaks.txt
    │   ├── Stringent.bed
    │   ├── Stringent_mspc_peaks.txt
    │   ├── TruePositive.bed
    │   ├── TruePositive_mspc_peaks.txt
    │   └── Weak.bed
    │   ├── Weak_mspc_peaks.txt
    └── rep2
        ├── Background.bed
        ├── Background_mspc_peaks.txt
        ├── Confirmed.bed
        ├── Confirmed_mspc_peaks.txt
        ├── Discarded.bed
        ├── Discarded_mspc_peaks.txt
        ├── FalsePositive.bed
        ├── FalsePositive_mspc_peaks.txt
        ├── Stringent.bed
        ├── Stringent_mspc_peaks.txt
        ├── TruePositive.bed
        ├── TruePositive_mspc_peaks.txt
        └── Weak.bed
        └── Weak_mspc_peaks.txt

BED files​

The *.bed files contain peaks in the standard BED format. These files contain peaks parsed from input files organized under the stringent, weak, background, confirmed, discarded, true-positive and false-positive groups. For example, peaks in a Confirmed.bed and Discarded.bed files may read is the following: 

$ head .\rep1\Confirmed.bed
chr     start   stop    name     -1xlog10(p-value)  strand
chr1    32600   32680   peak_4   4.08               .
chr1    32726   32936   peak_5   17.5               .
chr1    34689   34797   peak_6   5.82               .
chr1    35083   35124   peak_7   4.59               .
chr1    38593   38836   peak_8   10.7               .

$ head .\rep1\Discarded.bed
chr     start   stop    name     -1xlog10(p-value)  strand
chr1    137343  137383  peak_10  4.8                .
chr1    228585  228625  peak_12  4.37               .
chr1    265059  265115  peak_14  5.22               .
chr1    557793  557833  peak_29  4.16               .
chr1    725914  725963  peak_34  5.95               .

Accordingly, the peak named MACS_peak_4 is confirmed while a peak with MACS_peak_10 name is discarded.

MSPC Peaks​

The *_mspc_peaks.txt files group input peaks in different groups similar to the *.bed files. In addition, they contain information about the analysis performed on each peak. The additional information are:

  1. Combined probability of each peak that is X-squared of Fisher’s method;

  2. Right-tailed probability of the X-squared (represented in -Log10 (right-tailed probability);

  3. Benjamini–Hochberg corrected p-value (represented in -Log10 (Adjusted p-value).

For example, peaks corresponding to the above-mentioned peaks in the confirmed and discarded sets are as the following.

$ head .\rep1\Confirmed_mspc_peaks.txt
chr     start   stop    name      -1xlog10(p-value)  strand  xSqrd    -1xlog10(Right-Tail Probability)  -1xlog10(AdjustedP-value)
chr1    32600   32680   peak_4    4.08               .       222.936  46.359                            4.07
chr1    32726   32936   peak_5    17.5               .       284.738  59.674                            16.146
chr1    34689   34797   peak_6    5.82               .       74.005   14.49                             5.634
chr1    35083   35124   peak_7    4.59               .       52.867   10.042                            4.537
chr1    38593   38836   peak_8    10.7               .       121.576  24.609                            9.892

$ head .\rep1\Discarded_mspc_peaks.txt
chr     start   stop    name      -1xlog10(p-value)  strand  xSqrd   -1xlog10(Right-Tail Probability)  -1xlog10(AdjustedP-value)
chr1    137343  137383  peak_10   4.8                .       22.105  4.8                               NaN
chr1    228585  228625  peak_12   4.37               .       20.125  4.37                              NaN
chr1    265059  265115  peak_14   5.22               .       24.039  5.22                              NaN
chr1    557793  557833  peak_29   4.16               .       19.158  4.16                              NaN
chr1    725914  725963  peak_34   5.95               .       27.401  5.95                              NaN

Note that the first five columns are identical between *.bed and *_mspc_peaks.txt files, the columns 6, 7, and 8 are added in the *_mspc_peaks.txt files.

In order to reproduce these results, you may run the following commands:

wget -O demo.zip https://github.com/Genometric/Annotations/raw/master/SampleFiles/demo.zip; unzip demo.zip -d .
.\mspc.exe -i .\rep*.bed -r bio -w 1e-4 -s 1e-8

Log File​

This file contains the information, debugging messages, and exceptions that occurred during the execution. The files reads as the following: 

2021-03-09 15:47:22,524 [1] INFO    NOTE THAT THE LOG PATTERN IS: <Date> <#Thread> <Level> <Message>
2021-03-09 15:47:22,570 [1] INFO    Export Directory: C:\mspc\session_20210309_154722332
2021-03-09 15:47:22,572 [1] INFO    Degree of parallelism is set to 8.
2021-03-09 15:47:22,595 [1] INFO    .::...Parsing Samples....::.
2021-03-09 15:47:22,597 [1] INFO       #                Filename    Read peaks# Min p-value Mean p-value    Max p-value 
2021-03-09 15:47:22,597 [1] INFO    ----    --------------------    ----------- ----------- ------------    ----------- 
2021-03-09 15:47:22,906 [1] INFO    1/2 .\rep1.bed  53,697  2.239E-074  1.085E-003  1.000E-002  
2021-03-09 15:47:23,082 [1] INFO    2/2 .\rep2.bed  37,717  5.370E-301  1.520E-004  9.550E-003  
2021-03-09 15:47:23,084 [1] INFO    .::..Analyzing Samples...::.
2021-03-09 15:47:23,093 [5] INFO    [1/4] Initializing
2021-03-09 15:47:23,412 [5] INFO    [2/4] Processing samples
...
2021-03-09 15:47:23,749 [1] INFO    .::....Saving Results....::.
2021-03-09 15:47:26,162 [1] INFO    .::..Summary Statistics..::.
2021-03-09 15:47:26,163 [1] INFO       #                Filename    Read peaks# Background      Weak    Stringent   Confirmed   Discarded   TruePositive    FalsePositive   
2021-03-09 15:47:26,164 [1] INFO    ----    --------------------    ----------- ----------  --------    ---------   ---------   ---------   ------------    -------------   
2021-03-09 15:47:26,178 [1] INFO     1/2                    rep1         53,697     47.05%    42.95%       10.01%      26.84%      26.12%         26.84%            0.00%   
2021-03-09 15:47:26,191 [1] INFO     2/2                    rep2         37,717     16.30%    50.35%       33.35%      43.48%      40.22%         43.48%            0.00%   
2021-03-09 15:47:26,192 [1] INFO    .::.Consensus Peaks Count.::.
2021-03-09 15:47:26,192 [1] INFO    17,290
2021-03-09 15:47:26,193 [1] INFO    Elapsed time: 00:00:03.9396445
2021-03-09 15:47:26,193 [1] INFO    All processes successfully finished.

Note that the logs are reported in the following format: 

<Date> <#Thread> <Level> <Message>

  • Message is the description of each log entry;

  • Possible values for Level are INFO, DEBUG and ERR;

  • Thread is the number of the process thread MSPC used for executing each process. MSPC runs operations in parallel using n threads, where n is the degree of parallelism and reported at the beginning of the logs. It can be set via the -d | -degree-of-parallelism argument. This information is useful for debugging purposes only.

See Also​