how to handle duplicate reads in unpaired Whole Exome Sequence

Question

[adR]

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

Answer 1

[elisheva]

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.

[adR]

@elisheva,

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