Importing multiple demulitplexed files

I have demulitplexed 454 data that has already been sorted into folders. Should I import all the folders into Qiime separately and then merge later, or can I just concatenate all the files now? They are paired-end reads stored as fastq files.
Thanks in advance,

Hello Laura,

I think the best approach would be to keep your files in their current location, then import them all into Qiime using the fastq-manifest-format. This format supports paired and single end reads.

Let me know if you think this is a good fit for your data!



Hi Colin,
Just an update for you and others who are interested:
Importing using the fastq-manifest-format actually didn’t work, so I imported using the Casava 1.8 paired-end demultiplexed fastq format after moving all read files into the same folder.
Thanks for your response though!


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