There could be a technical problem or this might just be how you decided to construct the library. You can probably proceed with mapping, but first, review what this FastQC module does and make a decision based on that information.
FastQC manual: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Specifically: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/8%20Duplicate%20Sequences.html
Galaxy tutorials: https://galaxyproject.org/learn/
- NGS logistics - this is an introduction to Galaxy's functionality for the analysis of Next Generation Sequencing data.
- ChIP-seq: A simple ChIP-seq experiment with two replicates - an example analysis for finding transcription factor binding sites. Note the 50-60% duplicated levels in the sample data, and the filtering step after mapping to screen out multi-mapping sequences (possibly shorter/non-specific reads).
Thanks! Jen, Galaxy team