diff --git a/docs/documentation/minIon_workflow.md b/docs/documentation/minIon_workflow.md index f23c40c..3320eca 100644 --- a/docs/documentation/minIon_workflow.md +++ b/docs/documentation/minIon_workflow.md @@ -70,7 +70,7 @@ readsDir <- "ex3/read_dir_ex3" outDeplexSample <- file.path(outputDir, "dePlexSample") dir.create(outDeplexSample, recursive=T) -# load rename sample files and merge to a single file per sample if needed +# rename sample files and merge to a single file per sample if needed sampleTab <- read.delim(sampleFile, stringsAsFactors=F) dePlexSample <- mergeMinIONfiles(inDir=readsDir, outDir=outDeplexSample, sampleTab=sampleTab) @@ -110,5 +110,6 @@ finalTab <- createFinalHaplotypTableDADA2( minHaplotypCoverage = minCov, minReplicate = minOccHap, detectability = detectionLimit, minSampleCoverage = minCovSample, multithread=FALSE, pool="pseudo", OMEGA_A=1e-120) + +write.csv(finalTab, file=file.path(outputDir, "finalHaplotypList_vMinION.csv"), row.names=F) ``` -