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cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
https://cumc.github.io/xqtl-protocol/
MIT License
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Generate sample list & remove region list restriction #868

Closed wangyf1125 closed 6 months ago

wangyf1125 commented 6 months ago

Generate sample list in.txt file & remove region list restriction in trans analysis.

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gaow commented 6 months ago

@wangyf1125 why would you need to add a step to output sample list?

wangyf1125 commented 6 months ago

@gaow We might have this conversation before:

Yifei Wang: I am wondering if we need to keep a sample list as I need to construct E and G, and I want to keep the samples same with sumstats. If so, should I add this part in TensorQTL.ipynb or my own pipeline?

gaow: good point. In fine-mapping pipeline we do keep a list of samples that we actually analyze. I'm not sure how easy it is to add to tensorQTL pipeline but ideally yes it should go there.

So I suppose I could add a step to output sample list here?