I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have some experience how much of sample can I sequence in one run (by coverage around 30) and if it is really for this price?
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If it is a good idea to use PacBio depends a lot on what you want to sequence and what you want to do with the data you get. In short: you get longer reads but about 15% error per base. This means, you will have to cope with those errors, there are possibilities to do that. How much coverage you will get of you sample I cannot tell you, as I do not know what kind of sample you want to sequence.
How much data you get out of one SMRTcell depends also on the chemistry, I think it currently is between 275 Mb and 375 Mb, depending on chemistry. They have a nice brochure you could look at.
Anyway, you probably will have to get some advice by a bioinformatician of you choice on how to design and analyse your sequencing experiment.
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$\begingroup$ I am planning to sequence mouse genes of MHC a TLRs (about 2000 bp). Can you get me a fictitious example about how much sample can I involved by certain covarage?? Thanks a lot! ;) $\endgroup$ Commented Apr 4, 2014 at 12:35
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$\begingroup$ I have never done this calculation for a sample this small with PacBio. To keep it short, from one SMRTcell you would get 30x coverage of the E. coli genome (no fiction, they have done 3 cells and got 100x coverage). I guess this is a bit oversized for your short samples. Still, I would rather not do any more "virtual" calculations about this, you need to have someone you can talk to who understands your experiment and probably has seen more PacBio sequencing than I have. $\endgroup$ Commented Apr 4, 2014 at 14:14