3D-GBS, not suitable with pair3rad, because SE data

[edgagnon]

Hi, I'm running some tests, but pair3rad doesn't work for me really because I have SE data rather than PE. I get straight into error messages with cutadapt, which is expecting PE data.
I'm trying it now with gbs and rad options, but I don't have high hopes.

Originally posted by @edgagnon in #598

[isaacovercast]

Yeah pair3rad assumes your data is PE. If the samples are already demultiplexed then it would seem plausable to be able run it as ddrad

[edgagnon]

I'll give that a go and let you know if it worked or not. Le lun. 28 avr. 2025 à 14:03, Isaac Overcast ***@***.***> a écrit :

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*isaacovercast* left a comment (dereneaton/ipyrad#600) <#600 (comment)> Yeah pair3rad assumes your data is PE. If the samples are already demultiplexed then it would seem plausable to be able run it as ddrad — Reply to this email directly, view it on GitHub <#600 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALE6ZE7RWVLDTLHVQSMK7Z323ZUPXAVCNFSM6AAAAAB4BALWVSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMZWGA3DCNBQGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- --- *Dr. Edeline Gagnon* Assistant Professor Department of Integrative Biology University of Guelph (she/her)