Different read depth of sequencing.

[huangyizR]

Hi, Just wondering if I have multiple WGS data with different reads depth, do I need to standardized the reads depth by normal tissue?

Best, Peter

[veseshan]

FACETS analyzes single tumor-normal pair at a time. The log-ratio is a (local) ratio of tumor to normal depth. So standardization is built-in. But if you mean, should the library size of the normals be the same across different pairs, then no you don't.

[kobejamescurry]

@veseshan is it convinient for you to have a look at my issues, thanks a lot. I am really need your help

another one issue, can you clarify why the log OR is a symmetrical aixs, for a given loci, the log OR should be a certain value, why there has two , thanks a lot

[veseshan]

@kobejamescurry - You need to find another way of learning about genetics and assay technologies such as micro-array or sequencing rather than posting them as issues. This way you can understand concepts such as whether a snp in the population need to be heterozygous in a subject, phasing (which allele comes from which parental chromosome), assay's ability ability to detect polymorphism, sequencing depth etc.