[misterc]

Thank you for the reply . If I look at the specifications of HiSeq 2500, the sequence runtime in upto 6 days (in high output mode) which means that it has much longer cycle time as compared to HiSeq 4000. It generates smaller reads i.e. 2x125. Is it due to older technology or something else?
http://www.illumina.com/content/dam/...-portfolio.pdf

Hi Nauman,

Yes, HiSeq 2500 in High Output mode (v4) yields ~1TB of data in 6 days. This is due to capturing the data for each lane and surface in 3 passes instead of 2 like the HiSeq 4000. The HiSeq 2500's capable of running the v4 chemistry actually are scanning a little faster than the HiSeq 4000. That third pass to image each lane & surface (and the re-trace step) add up to about a 30 minute cycle time on HiSeq 2500. The chemistry isn't older at all, just an Illumina imposition to the supported read length.

[dorix]

The final answer for my problem is even more complicated, as I found out that my actual library size is different, as T-shaped adapters cause higher migration of libraries, as it is shown in TruSeq PCR-free manual... So real concentration is sth between and I have to asume library size or I should check it by testing amplification product size.

I hope it will help someone in the future.

[nahmed]

Base quality score pattern on illumina machines

Hi,
I have plotted the average base quality scores of a WGS DNA sequencing data from an Illuminia machine (see attachment). My question is, if I do another run to sequence a new sample on exactly the same machine with the same settings and the library preparation of the new sample is done in exactly the same manner, will I get "nearly" the same average base quality error pattern for the new sample.

[misterc]

Hi Nauman,

If your reagent lots are also the same, then yes you should get very similar results.