Question

Simulate 1, 3 Copies

1

Entering edit mode

13.0 years ago

Ann ▴ 10

Dear all,

Is there any tools that can simulate 1, 3, 7..CNVs?

Thanks!

Ann

next-gen sequencing • 2.4k views

ADD COMMENT • link updated 13.0 years ago by Ann • 0 • written 13.0 years ago by Ann ▴ 10

2

Entering edit mode

simulate reads? you need to provide more information on what it is you want to simulate.

ADD REPLY • link 13.0 years ago by Damian Kao 16k

score 1 · Answer 1 · 2011-12-20

1

Entering edit mode

13.0 years ago

Neilfws 49k

I suggest you search Google and/or PubMed for the terms "copy number variation" and "simulated data." There is a lot of literature on CNV detection and the authors often generate simulated data in order to test their algorithms. A good article will give details of the simulation process.

ADD COMMENT • link 13.0 years ago by Neilfws 49k

biobot 0.0.77.a.1099 · Answer 2 · 2011-12-20

0

Entering edit mode

13.0 years ago

Ann • 0

Thanks!

@DK: Sorry! I didn't give enough information, simulating paired-end reads.

I inserted and deleted some regions of fasta files to make CNVs of genes; after that Wgsim to simulate.

But I'd like to look for a software making real CNVs, especially: heterogeneous copy numbers.

ADD COMMENT • link updated 13.0 years ago by biobot 0.0.77.a.1099 6.2k • written 13.0 years ago by Ann • 0

0

Entering edit mode

If you have more information to add, please edit your original question instead of putting it here. This helps maintain the quality of Biotstar's answers. Thanks.

ADD REPLY • link 13.0 years ago by biobot 0.0.77.a.1099 6.2k