Reducing Number of Data Points for Circos Histogram

Question

[joshua.eunsong.craig]

Hello,

I am trying to make a coverage histogram using ClicO (Circos browser interface), however, I have too many lines. My data looks is in the form of a .txt, and was produced using bedtools genomecov function. It looks like this.

NC_009636.1 0   5   0

NC_009636.1 5   25  40

NC_009636.1 25  26  30

NC_009636.1 26  35  0

NC_009636.1 35  36  10

NC_009636.1 36  37  230

NC_009636.1 37  39  240

NC_009636.1 39  40  250

NC_009636.1 40  41  260
...

With a column for the chromosome data, start and stop coordinates, and coverage

I have over 300,000 lines, which I would like to bring down to below 25,000, preferable by increasing the bin width, which at the moment, are the start stop coordinates, some of them a single nucleotide long. I am trying to think of a way to do this in bash or R, and perhaps have bins be 100kb or so.

Best,

J

[ATpoint]

Please use the format bar and especially the code option (10101) to highlight code and data examples. I did it for you this time.