I am looking for biases in sequencing data that may appear at any step in the process of sequencing, caused by batch effects. For example, the impact of library prep on sequencing data. I know where these biases could occur, I just don't know what type of impacts they will have (impact coverage, GC content, etc).
Does anyone know of any papers which discuss this? I have found a few but mainly they just mention that they are correcting for batch effects but don't actually say what they are correcting.
Any help is much appreciated.