one lane or two lane in RNA-seq

[Pengfei Liu]

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!

[kwaraska]

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.