Query Regarding Generating Reads With Genome Coverage Values Of 1X, 2X Etc

Question

[Monzoor]

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.

Answer 1

[Jts]

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: https://github.com/jstjohn/SimSeq