Update README.md

ishworthapa · Aug 26, 2019 · 6075c13 · 6075c13
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Showing 1 changed file with 8 additions and 9 deletions.
diff --git a/README.md b/README.md
@@ -13,26 +13,25 @@ Following series of steps show how to run the DDR method on RNASeq data.
 ### Step0 Preprocess
 Step0 should be used to format the count table such that the input table has the gene expression table with first n columns as group1 samples (Triple negative:TN) and remaining columns as samples from group2 (other:OT). Rows represent the ENSG ids.
 ```
-cd src
-Rscript step0_preprocess.R
+Rscript src/step0_preprocess.R
 ```
 ### Step1 Calculate Stats
 In this step, the count table is normalized and the covariance, standard deviation, mean and MFC are being calculated.
 ```
-Rscript step1_calculateStats.R RNASeq
+Rscript src/step1_calculateStats.R RNASeq
 
 ```
 ### Step2 Find Reference set
 In this step, reference set of genes are being determined. The output file 'ref_cpm.csv' stores expression level of these reference genes.
 ```
-Rscript step2_findRef.R RNASeq
+Rscript src/step2_findRef.R RNASeq
 
 ```
 ### Step3 Find overlap using Fisher's Exact test
 #### Enter number of samples in first group as first input argument.
 Since the example dataset has 115 samples in group1.
 ```
-Rscript step3_overlapFisher.R 115 RNASeq
+Rscript src/step3_overlapFisher.R 115 RNASeq
 ```
 
 ## Output files
@@ -44,10 +43,10 @@ Rscript step3_overlapFisher.R 115 RNASeq
 ## Pipeline for microarray data. 
 ### Note that the steps are similar to that for RNASeq data. 
 ```
-Rscript step0_preprocess_microarray.R
-Rscript step1_calculateStats.R microarray 
-Rscript step2_findRef.R microarray
-Rscript step3_overlapFisher.R 115 microarray
+Rscript src/step0_preprocess_microarray.R
+Rscript src/step1_calculateStats.R microarray 
+Rscript src/step2_findRef.R microarray
+Rscript src/step3_overlapFisher.R 115 microarray
 ```
 
 ## Running all the steps together