Question: Query Regarding Generating Reads With Genome Coverage Values Of 1X, 2X Etc
gravatar for Monzoor
9.1 years ago by
Monzoor290 wrote:

I have a genome length of length approx 3 million basepairs. I need to generate 100 bp random reads so that the coverage is 1X.

Ideally how many reads should I output in the forward strand and how many in the reverse orientation. Should these numbers be equal.

genome read coverage sequencing • 1.9k views
ADD COMMENTlink modified 9.1 years ago by Jts1.2k • written 9.1 years ago by Monzoor290
gravatar for Jts
9.1 years ago by
Jts1.2k wrote:

1x coverage of a 3,000,000 bp genome is 3,000,000bp. Since you want 100bp reads, you want to generate 3000000/100 = 30000 reads. You should simulate the true sequencing process by randomly choosing the strand for each read. You will end up with approximately equal reads.

I would suggest not writing your own simulator however and use a tool like this:

ADD COMMENTlink written 9.1 years ago by Jts1.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 822 users visited in the last hour