I am having trouble using the app Mr DNA has to remove forward and reverse primer sequences from my raw, demultiplexed data. I follow the instructions (presumably quite well) that Mr DNA provides, yet for some reason when I attempt to combine all of my R1 and R2 files together and remove the primer sequences, it only generates a single empty "demux" folder and a sample-metadata.tsv files. Has anyone encountered this problem before?
I (a first-time doer of bioinformatics) am currently having exactly the same issue. Did you ever figure this out and/or find another better way to remove the primer sequences?
Found the problem. I am not afraid to admit that I forgot to unzip the files. I was trying to do this with fastq.gz files, not fastq files, whoops. Worked like a charm after that.