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Old 06-27-2013, 03:32 PM   #1
Kim_2013
Junior Member
 
Location: USA

Join Date: Jun 2013
Posts: 2
Default Barcoded primers for PacBio sequencing

Hi

I am going to use PacBio sequencer to sequence some community samples

I plan to take a variable region from 16S rRNA gene. I decided the primers but i am struggling with deciding the barcode.

I have many samples, and plan to use asymmetric barcodes for the insert of about 500bp. PacBio guideline recommends to use the recommended barcodes (they provided a recommendation list of about 48 pairs of 16 bp barcodes) but i really don't have idea how can i decide which barcode should be chose?

I checked the secondary structure of barcoded primers using http://www.idtdna.com/pages/scitools but don't know how can i judge the parameters? (self dimer, hair pin...)

Anyone can explain and teach me?. thank you so much!
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