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  • skander.hatira/biseps
  • irhs-bioinfo/biseps
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.test/comparison/comparisons.tsv
View file @ 876f9660
id control treatment
WT_vs_Meth13 .test/data/chr3test_a_thaliana_met13.CX_report,.test/data/chr3test_a_thaliana_met13.CX_report .test/data/chr3test_a_thaliana_wt.CX_report,.test/data/chr3test_a_thaliana_wt.CX_report
Delicia_vs_Annaglo /home/shatira/Delicia.deduplicated.bismark.cov.gz /home/shatira/Annaglo.TechRep_1.BioRep_2018-1.deduplicated.bismark.cov.gz
workflow/rules/methylation_extraction.smk
View file @ 876f9660
......@@ -5,7 +5,7 @@ rule methylation_extraction_bismark:
outdir+"results/{sample}-TechRep_{techrep}-BioRep_{biorep}/methylation_extraction_bismark/{sample}-TechRep_{techrep}-BioRep_{biorep}.deduplicated.CX_report.txt",
outdir+"results/{sample}-TechRep_{techrep}-BioRep_{biorep}/methylation_extraction_bismark/{sample}-TechRep_{techrep}-BioRep_{biorep}.deduplicated.bedGraph.gz",
report(expand(outdir+"results/{{sample}}-TechRep_{{techrep}}-BioRep_{{biorep}}/methylation_extraction_bismark/{{sample}}-TechRep_{{techrep}}-BioRep_{{biorep}}.deduplicated.M-bias_{R}.png", R=["R1","R2"]),category="M-Bias"),
temp(outdir+"results/{sample}-TechRep_{techrep}-BioRep_{biorep}/methylation_extraction_bismark/{sample}-TechRep_{techrep}-BioRep_{biorep}.deduplicated.bismark.cov.gz"),
outdir+"results/{sample}-TechRep_{techrep}-BioRep_{biorep}/methylation_extraction_bismark/{sample}-TechRep_{techrep}-BioRep_{biorep}.deduplicated.bismark.cov.gz",
outdir+'results/{sample}-TechRep_{techrep}-BioRep_{biorep}/methylation_extraction_bismark/{sample}-TechRep_{techrep}-BioRep_{biorep}.deduplicated_splitting_report.txt',
outdir+"results/{sample}-TechRep_{techrep}-BioRep_{biorep}/methylation_extraction_bismark/{sample}-TechRep_{techrep}-BioRep_{biorep}.deduplicated.M-bias.txt",
temp(expand(outdir+"results/{{sample}}-TechRep_{{techrep}}-BioRep_{{biorep}}/methylation_extraction_bismark/{context}_context_{{sample}}-TechRep_{{techrep}}-BioRep_{{biorep}}.deduplicated.txt",context = ['CHH','CHG','CpG']))
......
workflow/scripts/methylkit.R
View file @ 876f9660
library(methylKit)
library("tools")
### getting files ###
......@@ -32,7 +33,7 @@ readingReports=methRead(files,
treatment=c(rep(0,length(control)),rep(1,length(treatment))),
context=context,
mincov = minCov,
pipeline="bismarkCytosineReport",
pipeline=ifelse(file_ext(files[1]) == "gz","bismarkCoverage", "bismarkCytosineReport"),
dbtype = "tabix",
dbdir = snakemake@output[["methylDB"]]
)
......