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johli authored Apr 19, 2024
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## QTL data processing

The scripts in this folder are used to extract fine-mapped causal sQTLs, paQTLs and ipaQTLs from the results of the eQTL eQTL Catalogue, as well as construct distance- and expression-matched negative SNPs.<br/>
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The scripts in this folder are used to extract fine-mapped causal sQTLs, paQTLs and ipaQTLs from the results of the eQTL Catalogue, as well as construct distance- and expression-matched negative SNPs.<br/>

*Notes*:
- The pipeline requires the GTEx v8 (median) TPM matrix, which can be downloaded [here](https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz).<br/>
- The pipeline requires the GTEx v8 (median) TPM matrix, which can be downloaded [here](https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz).
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As a prerequisite to generating any of the QTL datasets, run the following scripts (in order):
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