Regular coverage in target capture sequencing

Question

[gubrins]

Heys, I'm working with target capture sequencing and currently I'm calculating the coverage of my target genes. I was wondering what is a regular coverage per gene in target capture sequencing. I would expect to have high values, as we are targeting specific areas, but I'm struggling to find information about it. Anybody working with this technique?

Thanks!

[GenoMax]

You have opened a number of related questions on this topic e.g.: Coverage of target genes

Have you not managed to make any progress on doing this analysis? There is no fixed number of how many reads one can expect to cover each base in case of targeted sequencing. One may be happy with 30 if you are interested in casual SNP's. If you are looking for rare variations then one may need 1000+ reads covering each base. Coverage would ultimately depend on the efficiency of targeting and amount of total sequence that you have generated.

As I recall you are working with an unusual genome so how did you decide your target genes/areas and what method did you use to target them? If you did this experiment right you must already have information about which regions you targeted and how to find them.

[gubrins]

Thanks for repplying! This question was more focused on getting an idea of how much coverage per gene is considered enough. I finally made progress and I got the coverage per gene, for this reason I was asking that. I'm working with a lizard's genome and I'm interested into amplifying mitochondria's genome and nuclear genes related in the OXPHOS project.