Yes, polyhedron, you can just change the adaptors you use to add an index onto your read. This is discussed in detail elsewhere in these forums. For PE reads, you only need to change PE adaptor 1. I'll give an example here:
+adaptor 1 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCTAACCT*T 3'
-adaptor 1 5' [Phos]-AGGTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT 3'
where the * is a phosphotioate and [Phos] is a phosphate when you order the oligos. You then need to anneal these two oligos together by mixing them to a final concentration of 15 uM each in TBS, heating them to 95C and cooling them slowly to room temperature to get the adaptor. Then you go ahead with the regular SE (with this adaptor) or PE (with the regular PE adaptor 2) sample preparation.
This essentially adds AACCT to the regular adaptors followed by the required T end, and thus your first six bases of read will be AACCTT. You need to be careful to balance out the A, C, G, T content of the first four bases of your adaptors so that the phasing and intensity levels are calculated correctly by the software. So, four indexes could be:
AACCTT
CCGGAT
GGTTGT
TTAACT
Others, feel free to correct me or improve on this comment. I'm only just beginning to do multiplex runs.
I will also add here (because I'm not a fan of how much Illumina charges for its kits) that New England Biolabs sells a kit that has everything in it for sample preparation except for the oligos for way cheaper than Illumina charges. Catalogue number E6000S or E6000L.
+adaptor 1 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCTAACCT*T 3'
-adaptor 1 5' [Phos]-AGGTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT 3'
where the * is a phosphotioate and [Phos] is a phosphate when you order the oligos. You then need to anneal these two oligos together by mixing them to a final concentration of 15 uM each in TBS, heating them to 95C and cooling them slowly to room temperature to get the adaptor. Then you go ahead with the regular SE (with this adaptor) or PE (with the regular PE adaptor 2) sample preparation.
This essentially adds AACCT to the regular adaptors followed by the required T end, and thus your first six bases of read will be AACCTT. You need to be careful to balance out the A, C, G, T content of the first four bases of your adaptors so that the phasing and intensity levels are calculated correctly by the software. So, four indexes could be:
AACCTT
CCGGAT
GGTTGT
TTAACT
Others, feel free to correct me or improve on this comment. I'm only just beginning to do multiplex runs.
I will also add here (because I'm not a fan of how much Illumina charges for its kits) that New England Biolabs sells a kit that has everything in it for sample preparation except for the oligos for way cheaper than Illumina charges. Catalogue number E6000S or E6000L.
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