Sequence Duplication Levels in targeted sequencing

Question

[Shaghayegh]

Hello,

I am processing some fastq files obtained from targeted sequencing using hybrid captures. I have run fastQC and I noticed all of my samples have over-represented sequences in the report. I have attached an example. This is the first time I am working with targeted sequencing data so I just want to make sure this is an expected case in targeted sequencing and not of concern because it does faithfully represent the input? Thanks for any input in advance

Answer 1

[Brian Bushnell]

Please describe your experiment in more detail. It sounds like everything was amplified, but if you could note the procedure, number of PCR cycles, etc, we might be able to help. The more data, the better; nobody here can help you from some random FastQC plot.