I have a project with two COI amplicons per sample. Do I have to analyze them separately, or there is a way that I can analyze them together as one amplicon? Thanks, Jin

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Hi,

I have a naive question. have a project with two COI amplicons per sample. Do I have to analyze them separately, or there is a way that I can analyze them together as one amplicon? If I can analyze the two amplicons as one, I would appreciate it if I could have a detailed instructions since I pretty new with Qiime.

Thanks,

Jin

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Hi @jlli2000,

This is a non-trivial problem. Do they belong to the same gene? The same database? Can you combine the database into a single map/database? If you can get them mapped to the same IDs, you could try sidle.

Best,
Justine

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Hi, Justine:

Thanks for the quick reply. Both amplicons are from COI gene. One is about 230 bp at 5' end of COI gene and the other is about 314 bp at 3' end of COI gene. There is no overlap between the two amplicons.

Thanks,

Jin

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Hi @jlli2000,

I think this would be a great application for Sidle. Feel free to ask questions here! I recommned installing the current version on Github, rather than a specific release.

Best,
Justine

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