How to generate random short sequences

[pony2001mx]

Dear all,

I need to generate some fake miRNAs as negative control. To speak more specificlly, I need to generate a few hundred random 21 nt - 24 nt sequences based on the genome fasta file.

What tools can be used here? Or what's the perl script that can complete this job?

Thank you very much for your help!!

[Liy]

Hi,

You can use bedtools random for example. You can specify the length and the number of intervals you want.

http://bedtools.readthedocs.org/en/latest/content/tools/random.html

or

Bedtools shuffle

http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html

L

[pony2001mx]

Hi Liy,

Thanks a lot! It's really what I need.

Best,

X