I am working on Illumina MiSeq sequence data. When I did quality analysis using FastQC it showed 97% of them are PCR duplicates. I went through FastQC documents, they say if the start and end position are the same, those sequences will be considered as PCR duplicates. What does base coverage and sequence coverage mean? How to remove PCR duplicates alone?
Hi Rohan,
Sorry for using the term pcr duplicates. FastQC shows 'sequence duplication level' as 93%. Even this seems to be odd. Attached is the fastqc report. My data is a paired end. I mapped them with my reference using BWA and used .bam file as an input for FastQC. I think, fastqc picks up the sequences with same start and end positions as duplicates. I used picard markduplicates. Even picard flags 93% sequence as duplicates. Am I missing anything. How can I mark only pcr duplicates.
Hi, Rohan and Oliver thanks for your suggestions. Yes my data is a tumour sample and now I understood the technical reason for the duplication.
The data is from Illumina and the reason for bad GC curve is, that particular exome has rich GC content.
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