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Old 05-12-2012, 01:53 PM   #1
mkdir
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Default Looking for a good illumina core facility

Hello, I am new to illumina sequencing. I am wondering how many total bases I can get if I spend ~ $3000 for PE 100 bp, one lane. And how many bases can be used after quality filtering. Are there any good illumina core facilities to recommend? Thanks a lot.
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Old 05-12-2012, 03:27 PM   #2
Wallysb01
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Originally Posted by mkdir View Post
Hello, I am new to illumina sequencing. I am wondering how many total bases I can get if I spend ~ $3000 for PE 100 bp, one lane. And how many bases can be used after quality filtering. Are there any good illumina core facilities to recommend? Thanks a lot.
A reasonable target for the newer version 3 kit would be ~120M 2x100 reads total. So that is about 24B bps. Illumina advertises less, but I've seen even more. After that it depends how strict a quality filter you want to impose. At Q20, you might only dump 10%, or less, but I've seen lanes were you dump nearly a ~1/3 of the bases, too. It just depends on how good your library is and how well clustering goes, and its pretty variable from my experience. That goes for total reads too, however. I've also seen lanes that apparently did not cluster well and gave "only" 70-80M reads. Its pretty impressive really, even when it doesn't work optimally.
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Old 05-13-2012, 10:53 AM   #3
scbaker
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Originally Posted by mkdir View Post
Hello, I am new to illumina sequencing. I am wondering how many total bases I can get if I spend ~ $3000 for PE 100 bp, one lane. And how many bases can be used after quality filtering. Are there any good illumina core facilities to recommend? Thanks a lot.
$3000 for a single lane of a HiSeq2000 run seems a little expensive to me (although if you're really only running a single sample like that, a service provider/core lab might have to charge more on a per lane basis). If you put your project up on BlueSEQ's exchange, several service providers will bid on it and you might end up getting a better price.

Good luck!
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Old 05-13-2012, 07:26 PM   #4
mkdir
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Hi Wallysb01 and scbaker, thank you very much for your helpful information.
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