Selection between Illumina Hiseq 2500 and NextSeq

Question

[ebrahimiet]

Hi, I want to send RNA samples of cancer cell lines for Illumina sequencing (100bp, paired end, 40 million reads per sample) Which machine is better Hiseq 2500 or NextSeq?

Thanks

Esmaeil

[Medhat]

Pros and cons of Illumina HiSeq and Next Seq

Sequencing platforms to compare

[Devon Ryan]

Whichever can do that for cheaper with your provider is the one to use. We also use (and run) both and both are fine for your needs.

Answer 1

[WouterDeCoster]

I assume your service provider will have a recommendation on this. I don't think that one machine is much better than the other, from your point of view the price matters maybe the most.

We use NextSeq for RNA-seq and are quite happy with it. The main difference perhaps (besides obviously throughput) is the two colour chemistry of NextSeq, which might result in high quality polyG stretches at the end of your reads, but those are easy to remove. Another difference is that on NextSeq you can go up to 150bp paired end, but apparently you already have made your mind up on that.

[User 59]

And you can go up to 250b PE on a HiSeq..

[WouterDeCoster]

Good catch. But only in rapid mode I see (http://www.illumina.com/systems/hiseq_2500_1500/performance_specifications.html). Which means that https://om.euformatics.com/apex/f?p=118:34:0::NO::P34_S1%2CP34_S2:NextSeq%20500%2CHiSeq%202500 isn't correct, thanks for pointing that out.