Importing and Merging additional samples (not from MiSeq)

Hi! I have a whole dataset in QIIME2 that I’ve run through various analyses with and I am very very pleased. This set was from a MiSeq run from whole bee guts. I also have some (~150) individual cultured isolates that I did 16S Sanger sequencing on myself. I put all of these sequences in a .fastq file and imported the sequences as FeatureData[Sequence]. So now I have a sequence list, but I don’t have any feature tables or anything. I am not sure if I am going about this the right way. Do you have suggestions for the best way to import two .fastq files, each containing ~50 sequences so that I can go through the same pipeline as I did qith MiSeq samples (i.e. open reference clustering, taxonomy) and then merge them with my exisiting data set to go through the alpha and beta diversity steps?

Thank you!

Hi @bmb22,

If the data are fastq, you should follow the same steps you did for your miseq data. You can use a manifest format to import these, pretending they represent a single sample. Then cluster OTUs, assign taxonomy, etc, as you did previously. You can use the feature-table merge method to merge the feature table you will get from OTU clustering.

I think you may be going the wrong way about this, though — those data are going to be vastly different from the miseq data, so I am not sure comparing the two in this way would be fruitful.

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