tsailabSJ / changeseq

CHANGE-seq analysis pipeline
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How to handle sample with a high duplication rate? #10

Open cissizhang opened 2 years ago

cissizhang commented 2 years ago

Hi, I have processed several samples with a high duplication rate (like ~40%). So I tried to deduplicate the sample after alignment by using picard. However, the read counts of on/off target sequences were significantly changed. I am wondering how the code handles the duplication. Does the deduplication step make sense? Thank you.