how to import already assembled trimmed reads in qiime2

[Florine Degrune]

Hi everyone one,

I have some difficulty understanding how to import reads that have been already trimmed and assembled into qiime2.

Here is the command:

qiime tools import \
  --type 'SampleData[JoinedSequencesWithQuality]' \
  --input-path manifest.csv \
  --output-path 03_reads_qza/reads_trimmed.qza \
  --input-format SingleEndFastqManifestPhred33V2

For the type, it seems to me right that it is joined sequence with quality, but for the output format, I am not sure. There is a list of many importable format, but I don't know which one correspond to my data. How can I determine the right input format ?

I also join the manifest file.

Thank you for your help !

Florine

[Robyn Wright]

Hi Florine,

 

For QIIME2 questions outside of the workflows and tutorials that we have on Microbiome Helper, I recommend asking on the QIIME2 forum. This is not something that I have experience with – maybe this will help? I don’t know what is in your manifest.csv file, but usually the way that you would import reads is by giving the path to where your files are, not a .csv file (e.g. step 1.5 in our SOP here).

 

Best wishes,

Robyn

 

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