From 2f6b9ce49bf1139f5600c42f356da784f8739209 Mon Sep 17 00:00:00 2001 From: Chris Nobles Date: Wed, 5 Aug 2015 12:04:29 -0400 Subject: [PATCH] Updated --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b94b13e..4b9d6f2 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ #### geneTherapyPatientReportMaker -For a specific patient, report integration near oncogenes and potentially expanded clones across cell types and multiple time points +For a specific patient, report integration near oncogenes and potentially expanded clones across cell types and multiple time points. Abundance by default is based on unique fragment length. #### Input A csv file such as `sampleName_GTSP.csv` to describe the replicates and the samples. @@ -43,7 +43,7 @@ GTSP0308-3,GTSP0308,pFR03 ``` Rscript makeGeneTherapyPatientReport.R #read in sampleName_GTSP.csv by default Rscript path/to/makeGeneTherapyPatientReport.R pFR03.csv #generated above -Rscript path/to/makeGeneTherapyPatientReport.R pFR03.csv -s #determine abundance by fragment length only +Rscript path/to/makeGeneTherapyPatientReport.R pFR03.csv -s #determine abundance by sonicLength package (Berry, C. 2012) ``` - 3 `check_gtsp_patient.R`: get trial and patient information for the GTSPxxxx folders