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xhhuanglab / OutcrossSeq

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How to use OutcrossSeq if there is no reference genome? #1

Open xiekunwhy opened 3 years ago

xiekunwhy commented 3 years ago

Hi,

In OutcrossSeq's paper, all demo species have a good quality reference genome, but most species are without a reference genome in practise, can OutcrossSeq deal with such datasets (for example, an F1 population genotype data generated from stacks (https://catchenlab.life.illinois.edu/stacks/) result)?

Best, Kun

mjchen-st commented 3 years ago

Hi, Without reference genome OutcrossSeq can't work well. We also compared genotyping using OutcrossSeq (whole-genome low-coverage resequencing) with that using a restriction enzyme-based method (target regions were enriched for sequencing) in other tree species. The two methods have their own applications and features, and they may serve different purposes in genetic studies. Best, Jojo