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@@ -379,18 +379,18 @@ Usage:
 
 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_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. 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