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Old 03-22-2011, 02:41 AM   #1
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Location: Oslo

Join Date: Mar 2011
Posts: 1
Default What is the minimum coverage needed?

Hi, (my very firs post here on this helpful forum

I have performed an experiment where I have placed individuals (from the wild) into new a environment, then I have sampled the individuals at different time points. I also have controlls for all the time intervals (individuals taken out of its common environment and placed back to similar conditions).
My plan is to sequence the mRNA on Illumina, potentially on a HiSeq2000 (but there is also a GA2 available).

I would be happy to get some suggestions reagrding coverage depth needed in order to aim at a certain number of individuals per lane (trying keeping the cost down). I am interrested in detecting active genes during a specific period in a defined environment, and to then, compare between different time stages. My study organism has about 21 000 genes, with a total of about 36Mb, and the genome has been sequenced (so I have a refrence genome). My plan is to go with paired end reads, and 50 or 75 bp.

Thanks in advance, this is all very new to me so all suggestions are welcome
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