Hi everyone, I'm new in metagenomic, I'm choosing V1-V2 for expose gut microbiome and i read some paper which discuss that V1-V2 is suitable for Lactobacillus, Bifidobacterium and some Bacillus species. What i did are:
1- I read this topic:Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt and use
SILVA_138_SSURef_NR99_tax_silva_trunc.fasta.gz.
2- Primer for V1-V2 is 27F:AGAGTTTGATCMTGGCTCAG and 338R:ACTGCTGCSYCCCGTAGGAGTCT.
3- I try this PCR tool (PCR Test) for quick test the primers and its ability to take V1-V2 of Lactobacillus, Bifidobacterium from 16s sequences in silva data.
And here the result is:
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So i wonder:
1- Should i test the primers like that?
2- If the result were right, how would i train classify by using 27F and 338R?
3- Tutorial for V1-V2 region?
.
Thank you so much !
Thanks for reaching out! Just as a heads up, I am re-categorizing this post in the 'General Discussion' category. Posts in this category are related to general questions about microbiome science, bioinformatics, or other general questions, ideas, or topics to discuss. Examples of posts include study design, paper discussion, etc. Posts in this category will not be triaged by a QIIME 2 Moderator.
I cannot advise on 1, but will leave that for other folks to chime in on - as far as 2 and 3, can you post those questions as two separate forum posts, to help us keep each topic clear and concise? You can post those two as user support questions, and myself or one of the other forum moderators will be happy to assist you there!
