When I run fastqc on my sample, it did not identify any adaptor sequence in the sample but there were some low quality reads in the sample. Then I used trim galore to remove the low quality reads using following command:
trim_galore --illumina --gzip --fastqc -o trimmed -j 4 --paired $Read1 $Read2
but in this when I checked the log file I was able to see some adaptors detected in the file. How is this possible? Are there any way to trim only low quality reads?
=== Summary === Total reads processed: 115,217,093 Reads with adapters: 40,928,868 (35.5%) Reads written (passing filters): 115,217,093 (100.0%) Total basepairs processed: 11,521,709,300 bp Quality-trimmed: 199,850,659 bp (1.7%) Total written (filtered): 11,118,622,037 bp (96.5%)