From 0775b801cc32029342e1325d55ac178956fe21cc Mon Sep 17 00:00:00 2001 From: Anita Lerch Date: Sun, 17 Nov 2024 21:10:50 -0500 Subject: [PATCH] Update minIon_workflow.md --- docs/documentation/minIon_workflow.md | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/docs/documentation/minIon_workflow.md b/docs/documentation/minIon_workflow.md index 6b12521..268107e 100644 --- a/docs/documentation/minIon_workflow.md +++ b/docs/documentation/minIon_workflow.md @@ -57,7 +57,10 @@ file.copy(from=system.file(package="HaplotypR", "extdata/ex3"), to=".", recursiv # List files example files in output direcoty dir(file.path("ex3")) ``` -The following files should be listed with the last R command: "marker_file.txt", "reads2_F.fastq.gz", "sample_file.txt". +The following files should be listed with the last R command: "marker_file.txt", "reads3.fastq.gz", "sample_file.txt". + + +WORK IN PROGRESS Run demultiplexing by sample and rename output files ```R @@ -92,12 +95,6 @@ dePlexMarker <- demultiplexByMarker(dePlexSample, markerTab, outDeplexMarker) write.table(dePlexMarker, file.path(outputDir, "demultiplexMarkerSummary.txt"), sep="\t", row.names=F) ``` -subset: remove markers without sufficient reads -```R -procReads <- procReads[procReads$numRead>10,] - -``` - Call Haplotypes ```R # call haplotype options