SOLiD

[jsun529]

Hi,

When check the unique.coverage.csv file of the genes, the average coverage is around 5000, how to link this to the actual X coverage that we usual say about NGS, for NGS it only ranges to ~ 100X , is that right ?
Does this have to take the length of the reference sequence into consideration?

Thanks,

[westerman]

When check the unique.coverage.csv file of the genes, the average coverage is around 5000, how to link this to the actual X coverage that we usual say about NGS, for NGS it only ranges to ~ 100X , is that right ?
Does this have to take the length of the reference sequence into consideration?

I don't see how the length of the reference should make a difference. If indeed you are averaging the counts (i.e., each line) within the unique.coverage.csv file and coming up with an average of 5000 reads (per base) then you have an incredibly high coverage. That is what you report. I am not sure where you are getting that the "usual" coverage for NGS is 100x. That is certainly a nice coverage level to have however my 'usual' (with large eukaryote genomes) is below that level.

[jsun529]

Thanks. Since we are doing targeted resequencing, for the unique.coverage.csv file, most of the position have 0 coverage, i am not sure if it is better to take the 0 out since we do targeted resequencing(only exons+/- small fraction) to do the average, or count it in if I include the 0 coverages then it will be around ~200X. Thanks.