Hi everyone, I was wondering if someone can point me to a good explanation where i can better understand how the reads in my fastq files are created. 

in the fastqc results from the data set I got, we assume that a lot of the adapter was sequenced ([2]. image). I'm not talking about read-thourgh, but the adapter somehow was sequenced. At least we think this is what we have. 

I have tried to understand in which direction the reads in my fastq files are read. ![example Overrep. sequences ([1]. image). What I don;t get is on which side do I find my adapters, if any are left?

Are they at the beginning of my read so should I crop head of the read, or should I trim the end of the of the read, as the adapters are there?

Is there a good explanation for that somewhere?

thanks 

george





![1]
![2]


  [1]: /media/images/dd7a724b-980d-4bd9-8291-5ee57fc3
  [2]: https://i.postimg.cc/9MZhcLMj/per-base-sequence-content.png
In Illumina sequencing adapter are always going to be present at 3'-end of the read (unless you are using some modification of standard procedure). You can also have adapter dimers (i.e no insert). That said, what kind of data is this. Looks like you can almost read the sequence looking at the plot so amplicons perhaps?