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Old 05-24-2011, 11:12 AM   #1
mgravina
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Default 5' versus 3' barcoding

Hello all. Can anyone offer insight into the pros and cons of placing index barcodes at the 5' versus the 3' end of the read?
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Old 05-24-2011, 11:37 AM   #2
epistatic
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5' of the read allows you to run multiplexed samples without doing the index read. I liked to do this on the GAII to avoid using the Paired-End module for SR multiplexing. Con is that the bases need to be balanced or you can throw off the cluster calling algorithms. Use cycle 5+ to avoid this type of problem.

3' end of read must mean the standard Illumina indexing method using a second priming and read to hit the index. That method works fine, extra reagents are in the SBS kits to allow for 7 cycles for the index read. Illumina only has 12-indexes for DNA and RNA out so far, so that would be a con. On the HiSeq this indexing read is easy to set up, I avoided it on the GAII.
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Old 05-25-2011, 11:16 AM   #3
mgravina
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Thanks for the info!
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Old 05-25-2011, 12:30 PM   #4
NextGenSeq
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Bioo has 48 barcodes using the 3' method. The kit works well.
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