F-seq output: Meaning of bed columns
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0
Entering edit mode
9.8 years ago

Hello,

I'm running F-Seq with output format bed. Does anybody know what is the meaning of the 5th column of the bed output?

Here's the command I've executed:

fseq -of bed -t 5 -l 800 -v -b $bff -d $bdir -o $outputdir

This is a sample of the output (first of 309072 lines):

chr10   95746   95753   chr10.1 0.012379828
chr10   95759   95762   chr10.2 0.012224182
chr10   95843   95866   chr10.3 0.0124211665
chr10   95872   95874   chr10.4 0.012203805
chr10   95981   95982   chr10.5 0.0121980915
chr10   95994   96150   chr10.6 0.014081057

The first 4 columns are self explanatory. But I can't get the meaning of the 5th, which ranges between 0.0121953 and 33.32249.

Thanks!

Dario

F-Seq fseq peak-calling • 2.8k views
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Entering edit mode

Hello, I get the same question as you did before, I want to ask if you have got the meaning of the 5th ? Thank you very much if I could get the answer, Thanks.

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1
Entering edit mode
9.8 years ago

in the source:

  private void doWrite() throws IOException {
    bw.write(chr + "\t" + _startPeakPos + "\t" + _currentPos + "\t" + (chr + "." + _counter++) + "\t" + _currentMax + "\n");
    _currentMax = 0.0f;
    _startPeakPos = 0l;
  }
}

currentMax is calculated as follow:

  public void writeDensity(float[] batch, int start, int length)
      throws IOException {
    int end = start + length;
    for(int i = start; i < end; ++i, ++_currentPos){
      if(!_aboveThreshold){
        if(batch[i] > _threshold){
          _aboveThreshold = true;
          _startPeakPos = _currentPos;
          _currentMax = batch[i];
        }
      }else{ // aboveThreshold
        if(batch[i] > _threshold){
          _currentMax = Math.max(_currentMax, batch[i]);
        }else{
          _aboveThreshold = false;
          doWrite();
        }
      }
    }
  }
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Entering edit mode

Thanks Pierre, I should have looked at the code myself. Although I was hoping for some simple interpretation of the 5th column and how to best use it... In case I'll dig into the code a little more...

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1
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5.4 years ago
vw ▴ 40

I just read the paper of F-seq and looking into the code. I think the 5th column appears the density of the peak. The F-seq applied the KDE to get the pdf function.

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