I recently started a new project with 2x250bp Illumina Reads. My FastQC files for the forward reads looked all pretty decent:
I then separate my reads into my specific libraries using cutadapt and furthermore demultiplex them using my barcodes without cutting them. Those files I import using qiime import and check them for their quality again and find this:
This is quite a problem for me because I usually cut at a Quality Score of 20 and then merge the paired reads using dada2. However, here for the first time I have to cut off at ~180bp and wont get a big enough overlap for successful merging. Of course I could include a few more bp with lesser quality but I dont really get where and how my sequences got so bad all of a sudden?