I know the equation is Coverage = (read length) (number of reads) / (haploid genome length) but am a little uncertain on what to put in each field (namely read #).
I have an organism with a genome 5,000,000 bp long, it's the only DNA I would be sequencing and I want to calculate the average fold coverage.
I'm using the NextSeq500.
This is where I am currently, but this doesn't look at all right.
C = LN / G
L = 150 bp
N = 130 x106
G = 5x106 bp
C = (150) (130,000,000) / 5,000,000
C = 3900
Hi Paige,
you're right in describing the way to get average coverage. but I wonder what is N made for? what 130 and 106 are presenting?
fred
Frederic Lepretre 130,000,000 is the max number of reads for the sequencing method
ok, 106 is in fact 10power6...
so you're wright, 3900 would be your mean depth.
but don't forget waste and trim that will reduce your sequencing data and low coverage of some regions as GC rich regions.
best
fred
Frederic Lepretre Okay, that value seemed high to me so I worried I was inputting the wrong value. 130 x 10^6 is the max possibly value, so I would expect the actual coverage to be lower than computed.
Thanks!
Paige Tears-Gladstone , size of the targeted genome is very small for high trouhgput sequencers we have now...
best
fred
yes, the formula is okay for calculating average coverage. but what is meant by max possible numbers of reads for the sequencing method? you must put in the actual numbers of reads that you obtained. Firstly, raw reads are needed to be trimmed, and mapped on the Ref genome. Then coverage is calculated based on mapped reads. Size of your targeted genome is very small that's why you are getting a high value.
Best wishes
Sawar
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA