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Old 01-10-2013, 06:28 PM   #1
Pengfei Liu
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Location: Beijing

Join Date: Nov 2012
Posts: 16
Unhappy one lane or two lane in RNA-seq

hi all,
I have RNA-seq project with 3 treatment and 4 replicates per treat, my supervisor want me to use MiSeq. But i find Miseq only get 7.5-8.0G data per lane, so I have to use run on two lanes for my samples. If I use HiSeq 2000, one lane could be enough.

I don't know if this will affect the results and reliability of the data if run on two lanes or two run?

Thanks!
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Old 01-11-2013, 04:41 AM   #2
kwaraska
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Location: Boston,MA

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One or two lanes will not affect your data as it is all sequence-not intensity based.

You can continue to run as many lanes as you want and continue to add data.

I will tell you that in my experience, that unless you are working with a very small organism, you will need ffar more data than even one lane of HiSeq will provide. For human/mouse, we generally run only 4 samples per HiSeq lane.
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