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Old 09-14-2012, 03:54 PM   #1
Junior Member
Location: Los angeles

Join Date: Sep 2012
Posts: 1
Question question about random select certain number of reads from ChIP-seq bed file

Hi everyone:
Now I want to normalize ChIP-seq bed file reads to certain number by randomly choose certain number of reads from the original bed file.
Dose anyone have such kind of scripts to do this? I tried to do the perl script by ran() operator. It will work for small bed file. But it will calculate forever if the reads if around 38 million. So is there any way I can unsort the @array element? So that I can use head to form a certain number of reads by randomly selection. Or Does anyone have better idea about that?

Thank you

Lijing is offline   Reply With Quote
Old 09-15-2012, 03:13 PM   #2
Senior Member
Location: Cambridge, UK

Join Date: May 2010
Posts: 311

Hi Lijing,

The (python) script below will downsample a file by writing out each line with probability p. E.g. if you want to sample a bed file from 38 million reads to 1 million p= 1/38 (~0.026):

Code: full.bed sampled.bed 0.026
You can optionally pass a 4th argument as seed to the random number generator to make the sampling repeatable.

It's not super-fast being Python but it shouldn't take more than few minutes for sampling a bed file of tens of millions of rows.

The code for


import sys
import random

if len(sys.argv) < 3 or len(sys.argv) > 5:
Sample lines from file.

USAGE: <file in> <file out> <p> <seed>
file in:  File to sample
file out: Output file
p:        Probability of a line to be sampled (sent to output)
seed :    (Optional) Seed to start the sequence of random numbers
p= float(sys.argv[3])
if p < 0 or p > 1:
    sys.exit('Invalid p (%s): p must be between 0 and 1' %(sys.argv[3]))

if len(sys.argv) == 5:
    rseed= sys.argv[4]
    rseed= None

fin= open(sys.argv[1])
fout= open(sys.argv[2], 'w')

for line in fin:
    prand= random.uniform(0,1)
    if prand <= p:

Hope it helps
dariober is offline   Reply With Quote

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