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Old 02-06-2012, 10:40 AM   #1
wingtec
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Default RNA-Seq on MiSeq

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
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Old 02-06-2012, 10:57 AM   #2
NextGenSeq
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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.
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Old 02-12-2012, 08:53 PM   #3
ScottC
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Isnt the new machine supposed to produce 7Gb for a 2x150b run? Doesn't that make it 7Gb/150b/2 reads = 23.3M clusters?
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Old 02-13-2012, 02:34 AM   #4
protist
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12 million reads is enough for bacteria and small euks..
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Old 02-13-2012, 03:33 AM   #5
kmcarr
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Quote:
Originally Posted by ScottC View Post
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.
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Old 02-13-2012, 01:12 PM   #6
ScottC
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Quote:
Originally Posted by kmcarr View Post
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.
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