Coverage calculation (on GA data)

[marlei]

Hi,

How to calculate coverage for Illumina Genome Analyzer sequencing data?

Wikipedia says: It can be calculated from the length of the original genome (G), the number of reads(N), and the average read length(L) as NL / G.

The question is how to get N?

Kind regards
Maria

[jgibbons1]

Hi Maria,
Is this de novo assembly or mapping?

If its de novo you can calculate Number of reads for each contig as follows

((coverage)*(length of contig)) / (read length)

Then you can multiply (TOTAL Number of reads) * (read length) / genome size

If you are mapping, you should be able to pull out the number of reads that uniquely map to the genome.

-John

[thinkRNA]

Hi Maria,
Is this de novo assembly or mapping?

If its de novo you can calculate Number of reads for each contig as follows

((coverage)*(length of contig)) / (read length)

Then you can multiply (TOTAL Number of reads) * (read length) / genome size

If you are mapping, you should be able to pull out the number of reads that uniquely map to the genome.

-John

Hi John, how do you pull out reads that map uniquely, I guess there is a flag in samformat for this? Also, what percentage of the reads that you map are duplicates and is there a way to distinguish these from PCR duplicates in RNA-seq data?
thanks so much!
Priyam