how to handle duplicate reads in unpaired Whole Exome Sequence
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2.2 years ago
adR ▴ 120

Hi all,

I was reading several posts on Biostar about read duplicates. However, I wasn't able to find/get a clear answer about :

  1. Whether it is necessary to remove duplicate reads or not?
  2. When should these read duplicates be removed (before alignment or after)?
  3. Also, what tool does a good job of removing duplicate reads?

Could someone please explain this to me. Thank you for your support!

Best
ADR

SAMtools PCR Picard • 628 views
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2.2 years ago
elisheva ▴ 120
  1. It is necessary to remove duplicate reads since you don't want the results to be biased.
  2. It's better to remove the reads after the alignment - when you get more information regarding their genomic positions.
  3. Try Picard.
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@elisheva,

Okay Picard might be good but do you think it is recommended for ATAC-seq?

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