Hi everyone - I’m about to run DADA2 as follows:
cd $WORK/Data/MSQ92/2_fastq
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-trim-left-f 13
–p-trim-left-r 13
–p-trunc-len-f 140
–p-trunc-len-r 140
–p-n-threads 32
–o-representative-sequences rep-seqs-dada.qza
–o-table table-dada.qza
–o-denoising-stats stats.qza \
I would like to specify the directory so that the rep-seqs-dada.qza and table-dada.qza files go to another folder called Merged_runs in my main Data folder.
I’ve tried using --output-dir Merged_Runs but it doesn’t work.
I’m stuck - any help would be much appreciated. Thanks!