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Old 02-05-2015, 09:35 AM   #7
AllSeq
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Quote:
Originally Posted by wingtec View Post
With all that said, if I am allowed to twist the question a bit.

Say, I already have some Affy microarray data and I want to better or at least confirm the array data with RNA-Seq. The Affy chip used was HG ST gene array and the experiment was done with n=3. Now we want to do also n=3 in RNA-Seq, will 20M clean read of PE2x100 have similar or better coverage than the array data?

Thanks

Wing
People have a lot of opinions on the amount of coverage needed for RNA-Seq - it almost turns into a religious debate! Generally speaking, 10M reads should give you 'array-like' coverage. 20M PE reads (which I'm defining as 20M clusters) would be even better. If cost is a major issue, you could either reduce the number of clusters or go for SE reads. PE is nice, but unless you're going to do the hard work of trying to figure out splice isoforms, it's probably not necessary.

Good luck with the experiment!
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