Random 24mers as control data-set
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
1 answer
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.
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