Apologies for the confusion, I started working with the joined (already merged samples), but then I have read from other forum posts that in order to use dada, and quality filtering it is advisable to work with the initial forward and reverse reads.
Doing so, I have decided to start with the initial forward and reverse form the different samples, using:
qiime tools import
And got this error:
An unexpected error has occurred:
**Forward and reverse reads must be provided exactly one time each for each sample. The following samples had forward but not reverse read fastq files: ECsample1_R1.fastq.gz, ECsample2_R1.fastq.gz + ALL THE SAMPLES
Is there a problem on the manifest? I have checked names and paths and it seems to be ok.
Should I check something else?