RNA-Seq on MiSeq

[wingtec]

Hi All,

Can you the experienced comment the use of MiSeq in doing RNA-Seq? Is the number of reads with MiSeq too little for RNA-Seq, esp for a big genome such as human? And, do people usually do Paired-end or single-end for RNA-Seq?

Thanks much,

Wingtec

[NextGenSeq]

Even with the upgrade I think you will get only 12 million reads, without it you get like 6 million.

This is only enough for micro-RNA-Seq which you could muliplex highly though.

[ScottC]

Isnt the new machine supposed to produce 7Gb for a 2x150b run? Doesn't that make it 7Gb/150b/2 reads = 23.3M clusters?

[protist]

12 million reads is enough for bacteria and small euks..

[kmcarr]

Isnt the new machine supposed to produce 7Gb for a 2x150b run? Doesn't that make it 7Gb/150b/2 reads = 23.3M clusters?

The 7Gb number mostly results from the increased read length, 2x250 so 7Gb/250bp/2 = 14M clusters.

[ScottC]

The 7Gb number mostly results from the increased read length, 2x250 so 7Gb/250bp/2 = 14M clusters.

Oh yes, of course, I forgot the 250b improvement.

Cheers,

Scott.