The coverage of re-sequencing sample

[ptongyoo]

Hi guys, I'm learning and planning to do the human genome re-sequencing project for identifying some structural variants.

I got many samples and base on my researched one sample is require one entire flow cell for 3X coverage. So, my question is how many coverage time is require for doing this, just 3 times coverage is enough for both entire genome re-sequencing and RNA-seq sequencing ?

[Melissa]

I'm not sure if I understand you correctly. Are you doing re-sequencing for the whole human genome? Since you have many samples, I guess you're considering targeted re-sequencing? But since you said one flow cell is estimated to give 3x coverage (3.2Gb x 3 = ~10Gb)... it sounds like you're sequencing the whole genome.

The easy way (but not the correct way) to estimate coverage is c = expected total amount of data/size of target. There's really no way to tell if you sequence an entire flow cell, you will get at least 3 reads at the each place. Therefore, I think 3x coverage is not sufficient. Anyway, I don't know what's the standard for re-sequencing so please don't listen to me!