Question: Understanding BEDtools summary output
0
gravatar for brismiller
3 months ago by
brismiller40
Bellingham, WA, USA
brismiller40 wrote:

Hey all,

I am using Bedtools summary program to do some quick quality control steps on some bed files that I have generated. I have looked for the man page for this program but I cannot find it. I am trying to understand what each of the columns in the output means. Is there a man page somewhere obvious that I am just not finding?

Any help would be appreciated,

Here is some example output:

chrom   num_records total_bp    chrom_frac_genome   frac_all_ivls   frac_all_bp min max mean
1   3286228 9027084 0.07738 0.077   0.077   1   277 2.747   
2   3616547 9811600 0.07528 0.084   0.084   1   220 2.713   
3   3035268 8212565 0.06163 0.071   0.070   1   152 2.706   
4   2912189 7962848 0.05912 0.068   0.068   1   213 2.734   
5   2705117 7333817 0.05642 0.063   0.063   1   193 2.711   
6   2602636 7250330 0.05309 0.061   0.062   1   163 2.786   
7   2352619 6513613 0.04953 0.055   0.056   1   186 2.769   
8   2356976 6090477 0.04511 0.055   0.052   1   164 2.584

I am mainly asking about these specific columns (chrom_frac_genome frac_all_ivls frac_all_bp min max mean)

man summary bed bedtools • 123 views
ADD COMMENTlink written 3 months ago by brismiller40

What is this program ? Can you add a link ? like a download page or something ?

ADD REPLYlink written 3 months ago by geek_y11k
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