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Hi everyone,
I am planning a ddRADseq experiment with non-model plants (this means, no reference genome available), and I am wondering how many reads should I get for to have enough coverage. I learned in a course that is good to aim for 35x coverage, because some reads are lost due to sequencing error and multiplexing error, so at the end you have ca. 20x coverage. In the course, they also gave us a formula to calculate the number or raw reads needed depending on the coverage: raw reads / samples / cut sites = coverage at each locus. However, how can I calculate the number of cut sites? I think I need a reference genome to do that, right? Also, I am not sure if the formula works for single RAD or also for ddRAD.
Thanks in advance for any help!!
I am planning a ddRADseq experiment with non-model plants (this means, no reference genome available), and I am wondering how many reads should I get for to have enough coverage. I learned in a course that is good to aim for 35x coverage, because some reads are lost due to sequencing error and multiplexing error, so at the end you have ca. 20x coverage. In the course, they also gave us a formula to calculate the number or raw reads needed depending on the coverage: raw reads / samples / cut sites = coverage at each locus. However, how can I calculate the number of cut sites? I think I need a reference genome to do that, right? Also, I am not sure if the formula works for single RAD or also for ddRAD.
Thanks in advance for any help!!