Question: Random extraction of restriction enzyme target sites from whole genome
0
gravatar for cfarmeri
4.5 years ago by
cfarmeri160
Japan
cfarmeri160 wrote:

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 toruble.
Thanks.

genome • 1.2k views
ADD COMMENTlink modified 4.4 years ago • written 4.5 years ago by cfarmeri160

Can you clarify what is there inside BED ? What do u mean by "finally extract fasta read from b.fasta ? After running getfasta ?

ADD REPLYlink written 4.4 years ago by geek_y11k

Thank you Goutham Atla. Sorry for not explaining enough.

I mapped original fastq reads to whole gemone by Bowtie2.
The BED you mentioned is this mapped bed file.

"What do u mean by "finally extract fasta read from b.fasta ? After running getfasta ?"
---Yes, after runnig fetfasta, I extract them  by grep.

Thank you

ADD REPLYlink written 4.4 years ago by cfarmeri160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1492 users visited in the last hour