coverage calculation

[arvi8689]

Hey

I am trying to sequence the exome and the capture kit is 100MB

The sequencing core promised 120 million reads per lane and we are using paired end 100bp reads and our fragment size is 250 basepairs.

My calculation was I will get 120 million reads * 200= 240 million bases read

so coverage= 240 million bases/100MB= 240x coverage (average)

But some people say I will get a coverage of only 120x. What could be the reason? Or is the coverage actually 240x?

[swbarnes2]

120 million reads, or 120 clusters?

60 million cluters will yield about 120 million reads.

[gringer]

The number of mappable reads will be less than the total number of reads, which may account for the difference.

As a side-note, does it make sense to include the total fragment size in coverage calculations, or should just the sequenced regions be used?