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.
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.