Hi Biostars

My original fastq reads have restriction enzyme target sequence at the head of each. (e.g. GGCCTTATATACATCGATCAAGATA......; GGCC is the restriction enzyme target site) and they have different length each other.

I would like to extract random reads from whole genome fasta. Each random read has the target site at the head and read length corresponding to original fastq reads.

(e.g. original: GGCCTTATATACATCGATCAAGATA, random: GGCCTTAAHCTAGATCGATCGCGT)

Now, I realize this random extraction by bedtools.

bedtools shuffle -i BED -g GENOME.FA > a.bed
bedtools getfasta -fi GENOME.FA -bed -fo b.fasta

Finaly, extract fasta reads with restriction enzyme target site from b.fasta by grep.

I mapped original fastq reads by Bowtie2. The BED file is this mapped bed by Bowtie2.

So this BED has sequence and length information corresponding to original fatstq.

But this processes are not necessary to get reads meeting my needs.

Anyone has efficient idea fitting my needs.

My English is not good but hope it doesn't cause any trouble.

Thanks