Question: What's the meaning of column "score" of output bed file from F-seq
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gravatar for vw
8 weeks ago by
vw20
vw20 wrote:

Hi all,

I am using F-seq to call peaks for ATAC-seq with output format bed. The first 5 columns of output bed file are:

chr1    3095526 3095786 chr1.1  0.04604167  
chr1    3100788 3101119 chr1.2  0.046266895 
chr1    3134777 3134941 chr1.3  0.035319872 
chr1    3249369 3249546 chr1.4  0.03644661  
chr1    3249710 3250211 chr1.5  0.1446483

Based on http://fureylab.web.unc.edu/software/fseq/, the 5th columns would be score, which Indicates how dark the peak will be displayed in the browser. But its type should be int. However, it is very clear that scores are float type in my output.

Thus, I am not pretty sure that the 5th column is the score mentioned by the above reference. If there anyone can tell me the exact meaning of the 5th column?

Thank you very much!

peakcalling atac-seq chip-seq • 119 views
ADD COMMENTlink written 8 weeks ago by vw20
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