Miseq illumina primer

rozitaa · 06-04-2013, 03:06 AM

Hi,

I am new here and also in sequencing area. I am not sure if I can ask such a basic question here or not. Actually, I'd like to sequence my 16S rRNA data for 3 different regions (v1-v3, v3-v5 and v6-v9). I have to design three different primer for sequencing with Miseq illumina system. I have read (Cporaso 2010 and 2012) papers but I have still problem with designing primers:

1- I don't know where I can find the Miseq illumina adaptor.
2- If it is some sequence constant for all regions or should be different.
3- How can I design the pad part.
4- The linker part.
5- The barcode
6- And also 12-base error-correctong Golay.

Could anyone explain them for me or any basic and advanced literatures I can learn from?!

Thanks,
Rozita

GenoMax · 06-04-2013, 04:02 AM

Here is an application note from Illumina that covers 16S sequencing on MiSeq: http://www.illumina.com/documents/pr..._miseq_16S.pdf

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06-04-2013, 03:06 AM	#1
rozitaa Member Location: Sweden Join Date: Jun 2013 Posts: 51	Miseq illumina primer Hi, I am new here and also in sequencing area. I am not sure if I can ask such a basic question here or not. Actually, I'd like to sequence my 16S rRNA data for 3 different regions (v1-v3, v3-v5 and v6-v9). I have to design three different primer for sequencing with Miseq illumina system. I have read (Cporaso 2010 and 2012) papers but I have still problem with designing primers: 1- I don't know where I can find the Miseq illumina adaptor. 2- If it is some sequence constant for all regions or should be different. 3- How can I design the pad part. 4- The linker part. 5- The barcode 6- And also 12-base error-correctong Golay. Could anyone explain them for me or any basic and advanced literatures I can learn from?! Thanks, Rozita

06-04-2013, 04:02 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	Here is an application note from Illumina that covers 16S sequencing on MiSeq: http://www.illumina.com/documents/pr..._miseq_16S.pdf