bokulich-lab / mishmash

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Pick out only variable region primers and avoid qPCR primers #14

Open lina-kim opened 1 month ago

lina-kim commented 1 month ago

Entirely regarding amplicon sequences.

Sub-issue 1: Variable region primers can be missed in certain text contexts.

V4-V5: 563 F (5′-nnnnnnnn-NNNNNNNNNNNN-AYTGGGYDTAAAGNG-3′) and 926 R (5′-nnnnnnnn-NNNNNNNNNNNN-CCGTCAATTYHTTTRAGT-3′)

Sub-issue 2: qPCR primers may be reported in addition to variable region primers.

0.2 μM of the universal bacterial primer 8 F (5′-AGAGTTTGATCCTGGCTCAG) and the broad-range bacterial primer 338 R (5′-TGCTGCCTCCCGTAGGAGT-3′)... Detection of the vanA gene was conducted via PCR performed using specific primers for the vanA gene: forward, 5′-AATCGGCAAGACAATATGAC; reverse, 5′-ACCTCGCCAACAACTAACGC.

Both examples taken from PMC7925583.