I have recently received some metagenomic data from 16S rrna sequencing. The sequencing company claim to have removed primers, however not adapter sequences. Please note that the files have been demultiplexed.
In the platform, we have forward and reverse strand fastq files. For each fastq file, there is information regarding the adapter used, for each strand.
However, when I run the following command:
cat myFastQ_forward.fastq | grep 'adapter_forward', it returns nothing. My question is, shouldn't the adapters be identified successfully simply by looking for an exact match in the fastq files? If not, why?