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In the specification sheet for the Illumina IIx upgrade, I see data output for 2x50 experiment as 9.5-12 GB. They specify that they are "high quality" reads because they pass v1.3 filters. Does anyone know what percentage of high quality reads are generally mappable to the reference genome?
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That is highly dependent on the quality of your library, the organism you're sequencing and the alignment algorithm you're using. As well as your definition of 'mapping' back to the genome.
For example with PhiX, you generally get greater than 98% of your reads mapping back to the genome using ELAND since you don't have to worry about reads in repeat regions or contamination. With human you'll get around 80% mapping back to the genome (depending on your library prep) using ELAND. The reason that the results for human are worse than PhiX is that ELAND only maps back unique alignments and the human genome sequence is highly repetitive (ie. any unknown region isn't going to align, and if you have the same sequence twice it won't count it unless it can resolve it's pair). ELAND also can't handle more than 2 errors in the seed it uses for the alignment so you lose some that way.
Hope this helps,
BradLast edited by basickler; 04-10-2009, 08:55 AM.
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