Continuing the discussion from Help with using cutadapt:
Hello,
I was able to figure out my error. I was just having some naming issues on my manifest file, there was a extra intended spacing. Just on another note tho, has this bug been solved yet? Cutadapt thinks my fastq.gz files aren't fastq.gz
because I am also facing the similar issue and now I am resorting to the plan cutadapt tool as you mentioned. My samples have been already demultiplexed for me and each sample has a R1 and R2 read for the forward and reverse reads respectively. And so, this is what I wrote for cutadapt:
cutadapt -a TCCTCCGCTTATTGATATGC --match-read-wildcards /home/qiime2/Greenhouse_experiment_2017/180612_BVDJ2/Gh_expt2017_A10{1,5}_S10{1,5}_L001_R1_001.fastq.gz > /home/qiime2/Greenhouse_experiment_2017/180612_BVDJ2/trimmed_16S/output.fastq
Does this look right? I want the standard output to go into a folder that I already made called "trimmed_16S".
Thanks in advance,
Max