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
•
written
by
ebrahimiet •
1 answer
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.
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.
Log in to answer this question.
-
RNAseq coverage vs depth for transcript isoform expression?
written by marineandriot •
-
Number of reads per lane
written by kamel •
-
Trimming Adaptor in Small RNA Analysis
written by ebrahimiet •
-
optimum number of short reads for denovo assembly
written by ebrahimiet •
-
grabbing the beginning and end of viral genome in denovo sequensing
written by ebrahimiet •
-
Increased duplication rates on chromosome 21
written by Daniel Gerlach •
-
Bowtie and % of RNA-Seq mappability.
written by tarek.mohamed
-
what is the Hiseq 2000 adaptor sequences
written by hana
-
Rnaseq: Read Length Different From Expected
written by thiesgehrmann •
-
Need Help For The Study Design Of A Rna-Seq Project
written by shirley0818
Pros and cons of Illumina HiSeq and Next Seq
Sequencing platforms to compare
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.