Question: Generate artificial reads
0
gravatar for finswimmer
3.0 years ago by
finswimmer14k
Germany
finswimmer14k wrote:

Hello,

i need to generate some artifical reads. randomsreads.sh from BBMap seems to be the right program for me.

I don't need random reads for my whole reference genome but for several thousand regions. So I wonder if there is better/faster way instead of first creating a separate ref file for every region? Maybe a new parameter for randomreads.sh for providing a bed file with the region (@Brian Bushnell :) )

fin swimmer

randomreads fastq bbmap • 676 views
ADD COMMENTlink modified 3.0 years ago by Joe18k • written 3.0 years ago by finswimmer14k
2
gravatar for James Ashmore
3.0 years ago by
James Ashmore3.0k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore3.0k wrote:

You can do this with bedtools and wgsim:

# Generate FASTA file of regions    
bedtools getfasta -fi reference.fasta -bed regions.bed > regions.fasta

# Generate reads from FASTA file of regions
wgsim regions.fasta reads_1.fastq reads_2.fastq
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by James Ashmore3.0k
2

Why not go back to randomreads.sh after bedtools getfasta. OP is happy with it otherwise :-)

ADD REPLYlink written 3.0 years ago by genomax92k

Good point, I'm not familiar with BBMap, either will work I guess

ADD REPLYlink written 3.0 years ago by James Ashmore3.0k

The combination with bedtools getfasta and randomreads.sh works perfect.

Thank you all.

fin swimmer

ADD REPLYlink written 3.0 years ago by finswimmer14k
0
gravatar for Joe
3.0 years ago by
Joe18k
United Kingdom
Joe18k wrote:

Haven't tried it personally, but ART is used a lot in my lab for this:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278762/

Not sure if it will do a region-by-region thing, though you could probably simulate a genome and then work backwards throwing away the uncessary stuff with bedtools or similar.

ADD COMMENTlink written 3.0 years ago by Joe18k
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