Illuminia Vs 454 Coverage Spread

Question

[wizard-14]

Hi all,

I'm just wondering about the difference in read numbers across samples on the Illumina miseq platform.

On the 454 analysis of the read numbers showed a tight bell shaped curve with a high peak. However with the Illumina miseq, the curve is much wider (the coverage varies from very high to very low). I understand that the Illumina gives a far rather number of reads but this doesn't explain the high degree of coverage variation across the samples

Does anyone know why this occur? Any methods to prevent the varying coverage?

Thanks in advance

[Phil S.]

Wouldn't you expect a far flatter curve from Illumina machines since you get way more reads (and therefore can picture a wider dynamic range)? Also, could you show the figures of the curves?

Answer 1

[Istvan Albert]

Since both methods generate a lot of data I don't think the shape of distribution would change, after all these are all very large samples already.

I suspect library preparation as the source of the discrepancy. Different amount of DNA ends up being sequenced for different samples.