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Originally posted by rskr View PostAnd you can do that with the 454 error model? Last I checked a mean quality of 30 would guarantee several errors in a 200-400bp read? Might be better off With a 250 base insert size and 150 bp paired end reads, with an overlapper that finds the intersection.
Also, to the extent that the quality values are accurate, software could use them to weight the likelihood of a given base being a true variation or not. Or, trivially, you could mask out bases that had quality values lower than 30.
Let's not ignore the elephant here: Illumina is producing 100's of gigabases of sequence per flow cell whereas a 454 run produces 100's of megabases. Illumina chemistry has a higher per run cost than 454, but we are still looking at something approaching a 100x price per base differential.
But the same logic applies to Sanger sequencing, which is at least 100x more expensive per base.
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Phillip
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Originally posted by rskr View PostWell except 454, would still fail to find linkage over 400bp consistently since the median read is much less, and with sufficient coverage paired end data is likely to find linkage up to 800bp which is maximum length PCR product.
If all goes well, a 454 run will have median read lengths >400 bases.
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Phillip
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Originally posted by pmiguel View PostHard to estimate total number of miscalls in a read from a mean quality value. But Q30 is one error per 1000 bases. So, as long as you don't have crazy high quality values off setting really low values, then I would not expect several errors in a 200-400bp read.
Also, to the extent that the quality values are accurate, software could use them to weight the likelihood of a given base being a true variation or not. Or, trivially, you could mask out bases that had quality values lower than 30.
Let's not ignore the elephant here: Illumina is producing 100's of gigabases of sequence per flow cell whereas a 454 run produces 100's of megabases. Illumina chemistry has a higher per run cost than 454, but we are still looking at something approaching a 100x price per base differential.
But the same logic applies to Sanger sequencing, which is at least 100x more expensive per base.
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Phillip
It's true that 454 is less cost effective than Illumina. Most applications can use the shorter read lengths obtained from Illumina/Solid, etc., and for those applications it makes a lot more sense to use those technologies. One thing to keep in mind, however, when comparing the amount of data produced--454 doesn't produce as much data, but in many cases, you don't need as much data with 454, either. Simply comparing numbers doesn't tell the whole story. RNA-seq provides an excellent example of where one technology might be better than the other, depending on your experiment. If you're trying to quantify gene expression, Illumina is definitely the way to. In that case, you're just trying to identify transcripts and count them. The high number of reads is a boon to your experiment. However, if you're looking for splice variants and don't care so much to quantify expression, 454 is probably a better technology. There will always be a niche for 454, although it's never going to be large.
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Originally posted by ajthomas View PostHowever, if you're looking for splice variants and don't care so much to quantify expression, 454 is probably a better technology. There will always be a niche for 454, although it's never going to be large.
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