I am using cutadapt (v1.14) to trim adapter from a published Ribosome profiling dataset (short single-end reads of 51 nt). When I run FastQC on the raw data, I see that the read quality is pretty good at the 3' end with the entire box plot of quality > 30. However when I trim the adapter and run FastQC on the processed data, I find that the Quality drops at the 3' end. I am unable to understand why there will be a drop in quality after adapter trimming when the original reads were of high quality. Would appreciate if someone could throw some light on this.
The adapter trimming command is as follows
cutadapt -a CTGTAGGCACCATCAATATCTCGTATGC -q 20 -m 20 -M 45 -O 6 -o SRR1562913_trimmed.fastq SRR1562913_1.fastq
FastQC on the raw data Raw dataset
FastQC on the processed data Processed data