Importing cleaned .fastq files

[AmeLaporte (Amelie Laporte)]

Hello everyone,
I have trouble for importing my fastq files as they are already filtered, trimmed etc I don’t know which command should I use in order to import my data and finish my analysis.

I don’t have access to the raw data so I can’t do the pipeline from the beginning.

Thank you for your help, Amélie.

[colinbrislawn (Colin J Brislawn)]

Hello Amélie,

I think you could import these files with using the fastq-manifest-format
https://docs.qiime2.org/2018.2/tutorials/importing/#fastq-manifest-formats

Let me know how well this guide works for you!

Colin

[AmeLaporte (Amelie Laporte)]

Hello Colin,
Thank you for your reply, but to create the manifest file I have to specify if the reads are forward or reverse. As they are already assembled, I don’t know what I should do…

[gregcaporaso]

Hi @AmeLaporte,
We have some notes on how to do this import here. @colinbrislawn is correct that you would use the fastq manifest format - you’ll just indicate “forward” for the direction of those files. Let us know if you run into any issues.