Physical/Fragment Coverage for Paired-Ends: Read Length

Question

[QVINTVS_FABIVS_MAXIMVS]

Very quick question:

I am using this method to calculate coverage:

Coverage = N_reads * (average_read_length / haploid_genome_size)

when calculating physical coverage for paired-ends, is "average_read_length" the average of the DNA fragment lengths (length of read1 + insert length + length of read2) or is it the length of the reads (read1+read2)

I think it's the fragment length/template length, right?

[piet]

Does "N_reads" represents the number of reads or the number of fragments/spots that were sequenced?

[GenoMax]

You would not know the length of the fragment. It would be plain average_read_length in terms of bases. This would be a rough estimate of coverage for the genome based on the number of bases you sequenced and the size of the genome. The formula may need to be Coverage = (N_reads * average_read_length) / haploid_genome_size

Answer 1

[Devon Ryan]

It depends on what sort of coverage you want to calculate. If you're doing variant calling, then you care about how many reads are providing information about the bases at each position, so just the average read length (or sum of reads for PE datasets). If you're doing something like peak calling then you care more about how much data can be used to find peaks, so you'd use the fragment length.