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Old 09-13-2011, 08:25 PM   #4
son_nexg
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Location: Australia

Join Date: Jul 2011
Posts: 8
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Thanks for your reply 'robs'.

I will have a look at the literature on this.
I was just wondering about it ... so far I was dealing with the DNA seq data and I would expect roughly 10% duplicates in a typical run. But with RNA-seq the story is little different. We start with a very-2 low amount of starting ploy-A capture RNA and then have to amplify it many fold to get decent amount for the sequencing run. Which makes it more prune to having PCR duplicates in the final data.

I can see people are working on protocols for transcriptome data where you can do away with PCR amplification step (e.g. http://www.nature.com/nmeth/journal/...meth.1417.html) but as of now Illumina's protocols use PCR and we need to have reasonal filters to get some real information out of the sequence data.
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