Understanding BEDtools summary output
0
1
Entering edit mode
3.8 years ago
brismiller ▴ 50

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)

bedtools bed summary man • 943 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 3054 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6