Random 24mers as control data-set

Question

[asumani]

Hi all,

I am working with 24nt siRNA. I downloaded sRNA data online, aligned my reads to miRNA.fa and extracted unaligned reads. Then I converted bam to fastq and I extracted only 24nt length reads.

For statistical analysis I want to have random 24mers as control data-set. Any suggestion for how to perform that?

Thanks, Asuman

Answer 1

[GenoMax]

You could write a program yourself to generate random 24mers but something like the following from BBMap suite may help.

randomreads.sh -Xmx10g ref=your_seq.fa out=stdout.fa minlength=24 maxlength=24 reads=20 | grep -v "^>" > random_24mers

Change reads= to a large number you need/want. You can sort/uniq the output if you want to get unique kmers.

[asumani]

It just helped perfectly indeed. Many thanks!