Help with pipeline

I am new to qiime2 so pardon me if my terminology is off. I am trying to integrate my data into the pipeline to generate OTUs for a set of nanopore data. The data that I have looks like this:

I5_8_I7_9.1 bc=TGTTCCGTCGGCTAAT
TGTT…[more sequence]…TGACT
I5_8_I7_9.2 bc=TGTTCCGTCGGCTAAT
TGTT…[more sequence]…CGTT

Where each line is a sequence from a single barcode mapped back to a given sample (called I5_8_I7_9). I have a total of 24 samples mapped. I created a map file that looks like this:

|#SampleID|BarcodeSequence|LinkerPrimerSequence|Subject|Edge 50m|Edge 100m|Year|Age|Sex|
|#q2:types|categorical|categorical|categorical|Categorical|Categorical|numeric|categorical|categorical|
|I5_8_I7_9|TGTTCCGTCGGCTAAT|CACTCTTTCCCTACACGACGCTCTTCCGATC|CF2001|E|E|2015|Adult|Female|
etc…

I have hit a road block. I have no idea how I take this data and use Qiime to call OTUs for each of my samples. I have read the tutorials, but they all start at the fastq file and go through deblur and denoise which is not what I have right now. I have been using the qiime 2 studio and also the command line but have only gotten so far as to import my sequence file into a FeatureData[Sequence]. Please help!

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Hello @Maxy!

Welcome! :houses:

This format you provided a snippet of is almost a QIIME 1 style seqs.fna file, the only difference is that your reads are delimited with a period (.) instead of an underscore (_). If you were able to edit this file to make labels like this: I5_8_I7_9_1, you would be able to follow the OTU clustering tutorial, directly!

That sounds like a lot of work, though — is there any chance you have the original fastq files around? That would open up a lot more opportunities for analysis.

Keep us posted! :t_rex: :qiime2:

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Thank you. This seemed to work, I’m still struggling with other things still but I got through the OTU clustering. Honestly I am trying to figure out how to generate one of those nice taxonomic barplots for my samples and/or a PCoA. I will probably be back here again.

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