Coverage calculation needed for target enrichment

[Mary_R]

Hi all,

I have libraries with and insert size around 200bp that were afterwards target enrichted for 5000snp. Each of the 5,000 SNP included a final flanking sequence length of 60 bp on either side of the SNP so each locus consists of 120 bp. Now I need to calculate the output I need for a 1x coverage and I have a really stupid doubt. Can you please tell me if I need to use the size the locus (120bp) or the insert size of the library in my calculations?

As an example:
5000snp x 120bp= 600000bp so I will need 0.0006GB to have 1x coverage
Or
5000snp*200bp=1000000, so I will need 0.001GB to have 1x coverage

Can you kindly help me to understand what is the right calculation?
Thank you so much

[BioDynami]

Hi Mary,

Coverage is based on your library insert size (200 bp) since this is the actual sequencing data you will get.