For Amplicon Sequencing it is known that a lot of reads will have the same start position. But this is more due to Amplicon sequencing than the Proton.
But how high should the percentage be for Whole Exome Sequencing using the Proton protocols ? I have been seeing values up to 80% or more (using Picard), which seems a bit much. But it could also be due to using single end reads.
Also how to deal with duplicates in Amplicon data ? I have been thinking about removing optical duplicates only.
But how high should the percentage be for Whole Exome Sequencing using the Proton protocols ? I have been seeing values up to 80% or more (using Picard), which seems a bit much. But it could also be due to using single end reads.
Also how to deal with duplicates in Amplicon data ? I have been thinking about removing optical duplicates only.
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