RNA-seq on MiSeq - enough depth of cover for a novel 500 MB genome?

[DrYak]

Hi,

I'm looking to do DGE on an eukaryotic genome of around 450-500MB. It is on an unsequenced species although there are related species that have draft and transcriptome data available. I was planning on doing the four sequences separately for DGE and then pooling the data to make a ref transcriptome.

The company I'm dealing with says they can give me 3-5 million reads per sample on the MiSeq. I'm concerned that this will not give me enough depth of coverage to get any robust differences.

Are my concerns warranted? I would hate to spend all that money and not get interpretable data.

[Martin_Ranik]

You're probably better off doing some HiSeq. The /Gb cost is much less than MiSeq. You could multiplex your samples and do a hiseq lane, try to make a de novo assembly, map to it to obtain expression data. If the gene expression data depth is insufficient for your needs, you could do another lane or two.

[scbaker]

You're probably better off doing some HiSeq. The /Gb cost is much less than MiSeq. You could multiplex your samples and do a hiseq lane, try to make a de novo assembly, map to it to obtain expression data. If the gene expression data depth is insufficient for your needs, you could do another lane or two.

I agree. If you're outsourcing the project, there's absolutely no reason not to pick the best instrument for the job. I'd look for a provider that has a HiSeq.