I am trimming the adapters of my data, for one of the controls cutadapt It's only keeping the 5.2% of the reads after trimming and removing reads shorter than 17bp
$ cutadapt -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG -j 4 -m 17 -o control_2_trimmed.fastq control_2.fastq === Summary === Total reads processed: 5,252,641 Reads with adapters: 5,169,644 (98.4%) Reads that were too short: 4,981,734 (94.8%) Reads written (passing filters): 270,907 (5.2%) Total basepairs processed: 262,632,050 bp Total written (filtered): 8,801,796 bp (3.4%)
While for the other samples values around 40% are obtained. Is the problem somehow my foult or coud It be from the data?
Thank you in advance, Jose