I learn from this post that Libraries prepared with Illumina library prep kits require adapter trimming only on the 3’ ends of reads, because adapter sequences are not found on the 5’ ends.
However, when we use tools like cutadapt, options are available for removing sequence of an adapter ligated to the 5' end of first or second mate.
It looked confusing to me. Did I make some misunderstanding on this issue?
My guess is that sequencing can also start from the adapter before the first base of the DNA insert in Reads 1 and 2. Am I right?