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Old 07-28-2015, 12:00 AM   #1
hartmaleon
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Location: Melbourne

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Default Newbie question: Seq company barcode library size

Hello fellow SEQers,

Although there are millions of unique combinations possible for a 12-base barcode, I expect that sequencing companies use a much smaller collection.

Can someone please give me an idea of the number of barcodes a sequencing company 'typically' uses e.g. <100, 100-200, >200 etc

Thanks in advance,
Leon
(Bioscience undergrad)
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Old 07-28-2015, 01:16 AM   #2
nucacidhunter
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Most companies use 6-8 base indexes for their library preps. 12 base indexes mostly have been used in non-kitted protocols. Index can be in one of adapters (single index) or two (dual index). For one type of library up to 384 indexes are available. One company might have different indexes for different products for instance Illumina’s small RNAseq libraries use different indexes than RNAseq libraries. Some new products are coming to market that uses thousands of barcodes to mark library fragments originating from a large genomic regions or single cells.
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Old 07-28-2015, 01:49 AM   #3
hartmaleon
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Thanks for the quick response

I was asking because I'm looking at some legacy 454 DNA sequences to learn about sequencing and sequence data processing. I noticed that among the sequences from 100 samples from one experiment, some barcodes were used twice (sequencing must have been split across two runs to avoid confusion).
Anyway, I just assumed that the sequencing company had insufficient barcodes to apply unique codes to each sample, but from what you're saying, it seems they should have been able to do this.

Thanks again
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Old 07-28-2015, 02:05 AM   #4
nucacidhunter
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I have not work with 454 for long time but I think their barcodes were limited. They could have run libraries with the same barcode in separate Picotiter plates or could have run in the same plate using divider.
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