F-seq output: Meaning of bed columns
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
2 answers
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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Ram
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Pierre Lindenbaum
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written
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Pierre Lindenbaum
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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.