Fixed a minor bug which only affects paired-end reads for reporting how many alignmen...

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 4b0b3ec6bbea187f13a41dfeb8fb873aaa3b1d36..7b9a4b83ca83a7ec87926af31cab8bf292a29e8c 100644 (file)
--- a/README.md
+++ b/README.md
@@ -375,22 +375,22 @@ you.
 
 Usage: 
 
-    rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_sample_condition1 FDR_rate output_file
+    rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_of_samples_in_condition_1 FDR_rate output_file
 
 This script calls EBSeq to find differentially expressed genes/transcripts in two conditions.
 
-data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.
-[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.
-number_sample_condition1: the number of samples in condition 1. A condition's samples must be adjacent. The left group of samples are defined as condition 1.
-FDR_rate: false discovery rate.
-output_file: the output file.
+data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.   
+[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.   
+number_of_samples_in_condition_1: the number of samples in condition 1. A condition's samples must be adjacent. The left group of samples are defined as condition 1.   
+FDR_rate: false discovery rate.   
+output_file: the output file. Three files will be generated: 'output_file', 'output_file.hard_threshold' and 'output_file.all'. The first file reports all DE genes/transcripts using a soft threshold (calculated by crit_func in EBSeq). The second file reports all DE genes/transcripts using a hard threshold (only report if PPEE <= fdr). The third file reports all genes/transcripts. The first file is recommended to be used as DE results because it generally contains more called genes/transcripts.   
 
 The results are written as a matrix with row and column names. The row names are the differentially expressed transcripts'/genes' ids. The column names are 'PPEE', 'PPDE', 'PostFC' and 'RealFC'.
 
-PPEE: posterior probability of being equally expressed.
-PPDE: posterior probability of being differentially expressed.
-PostFC: posterior fold change (condition 1 over condition2).
-RealFC: real fold change (condition 1 over condition2).
+PPEE: posterior probability of being equally expressed.   
+PPDE: posterior probability of being differentially expressed.   
+PostFC: posterior fold change (condition 1 over condition2).   
+RealFC: real fold change (condition 1 over condition2).   
 
 To get the above usage information, type 
 
@@ -415,6 +415,8 @@ differential expression analysis.
 
 We thank earonesty for contributing patches.
 
+We thank Han Lin for suggesting possible fixes. 
+
 ## <a name="license"></a> License
 
 RSEM is licensed under the [GNU General Public License