RNA-Seq by MinION

Question

[Deepblue]

Hi all,

I would like to use MinION for RNA-seq analysis for more than 20 samples of baker's yeast. I am wondering if anybody has ever tried barcoding kit to do multiplexing RNA-Seq? The output per flow cell is between 7-12 M reads in general, and if I use maximum 12 barcoding capacity of barkoding kit per flow cell on MinION, around 1 M per sample is generated. But, it is unclear to me whether this read depth is enough for differential gene expression analysis as it generates long reads, while Ilumina reads are short, but 5 to 10 M reads and more are generally generated. Any suggestions would greatly help me in making decision.

Thank you.

Answer 1

[colindaven]

I think the relative efficiency of the barcoding itself will lead to much greater impacts on the experiment than purely thinking about the number of reads. While I'm a big fan of nanopore for genomics and especially epigenomics, I haven't seen great Differential Expression data so far. I think the short read competition is far better and shows more stable performance, unless you're looking at long novel isoforms which are hopeless to assess with short reads.

Remember the rRNA depletion steps whatever you decide to do.