The Nextflow pipeline for Splicing Quantitative Trait Loci (sQTL) mapping
public
1yr ago
Version:
Version 1
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A pipeline for splicing quantitative trait loci (sQTL) mapping. Splicing quantitative trait loci mapping is a technique used to identify genetic variants that affect the splicing of RNA transcripts and how they contribute to complex traits.
The pipeline performs the following analysis steps:
- Index the genotype file
- Preprocess the transcript expression data
- Test for association between splicing ratios and genetic variants in cis (nominal pass)
- Obtain an empirical P-value for each phenotype (permutation pass, optional)
- Control for multiple testing
Code Snippets
165 166 167 168 | """ index_geno.R --genotype_file $genotype """ |
193 194 195 196 | """ prepare_trexp.R --group "$group" -t $te -m $metadata --gene_location $genes --covariates --output_tre tre.df.RData --output_gene genes.ss.bed --output_cov covariates.df.RData """ |
198 199 200 201 | """ prepare_trexp.R --group "$group" -t $te -m $metadata --gene_location $genes --output_tre tre.df.RData --output_gene genes.ss.bed --output_cov covariates.df.RData """ |
226 227 228 229 230 | """ res=\$(echo $chunk | sed 's/_in/_out/') sqtlseeker.R -t $tre_rdata -i $indexed_geno -l $chunk -c $cov_rdata --asympt --ld ${params.ld} -o \$res """ |
232 233 234 235 236 | """ res=\$(echo $chunk | sed 's/_in/_out/') sqtlseeker.R -t $tre_rdata -i $indexed_geno -l $chunk -c $cov_rdata --asympt --svqtl --ld ${params.ld} --window ${params.win} -o \$res """ |
253 254 255 256 | """ sqtls.R -n all-tests.nominal.tsv -f ${params.fdr} --rm_svqtl --md_min ${params.min_md} -o sqtls-${params.fdr}fdr.nominal.tsv """ |
278 279 280 281 282 | """ res=\$(echo $chunk | sed 's/_in/_out/') sqtlseeker.p.R -t $tre_rdata -i $indexed_geno -l $chunk -c $cov_rdata -M ${params.max_perm} --window ${params.win} -o \$res """ |
302 303 304 305 | """ sqtls.p.R -n all-tests.nominal.tsv -p all-tests.permuted.tsv -f ${params.fdr} --rm_svqtl --md_min ${params.min_md} -o sqtls-${params.fdr}fdr.permuted.tsv """ |
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Created: 1yr ago
Updated: 1yr ago
Maitainers:
public
URL:
https://github.com/guigolab/sqtlseeker2-nf.git
Name:
sqtlseeker2-nf
Version:
Version 1
Downloaded:
0
Copyright:
Public Domain
License:
GNU General Public License v3.0
Keywords:
10.1038/s41467-020-20578-2
- Future updates
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