I have forward and reverse single end reads. I can distinguish them from fastq file according to a forward or a reversed primer. However, I do not understand how one can get reversed and forward single end reads from the sequencing. If I look at the forward reads in FastQC, the per-base quality looks good, if I look at reverse reads, the per-base quality degrades faster.
I thought that from the sequencing we get only one read of the form: forward primer - fragment of interest - reverse primer as exactly on this pic below. Why in fact do I have reverse and forward reads identified by primer then?