Exome sequencing one sample on two lanes considered two read groups for marking of PCR duplicates?
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6 weeks ago
rebeliscu ▴ 30

I'm asking because I don't know whether to mark different lanes as a different library for the purpose of marking PCR duplicates. My instinct is that different lanes from the same library should still be treated as a single read group, since PCR duplicates could be found across lanes, no?

Thanks in advance.

deduplication read groups exome sequencing • 223 views
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If it is the same library that run on two lanes then it is a technical sequencing replicate.

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Sorry, I'm somewhat new to all of this. Does that imply PCR duplicate and thus the presence of duplicate reads should be considered across lanes?

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Yes because it is the same library running on different lanes to get more data.

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