Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcr...

[rsem.git] / rsem-run-ebseq

diff --git a/rsem-run-ebseq b/rsem-run-ebseq
index c4140c53551f6be26ad23435194edff2dd609cc5..9693eeea13e550f63879514173a346c328dbc66d 100755 (executable)
--- a/rsem-run-ebseq
+++ b/rsem-run-ebseq
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
@@ -85,14 +85,18 @@ This program is a wrapper over EBSeq. It performs differential expression analys
 
 This file reports the calculated statistics for all genes/transcripts. It is written as a matrix with row and column names. The row names are the genes'/transcripts' names. The column names are for the reported statistics.
 
-If there are only 2 different conditions among the samples, four statistics (columns) will be reported for each gene/transcript. They are "PPEE", "PPDE", "PostFC" and "RealFC". "PPEE" is the posterior probability (estimated by EBSeq) that a gene/transcript is equally expressed. "PPDE" is the posterior probability that a gene/transcript is differentially expressed. "PostFC" is the posterior fold change (condition 1 over condition2) for a gene/transcript. It is defined as the ratio between posterior mean expression estimates of the gene/transcript for each condition. "RealFC" is the real fold change (condition 1 over condition2) for a gene/transcript.  It is the ratio of the normalized within condition 1 mean count over normalized within condition 2 mean count for the gene/transcript. Fold changes are calculated using EBSeq's 'PostFC' function. The genes/transcripts are reported in descending order of their "PPDE" values. 
-  
+If there are only 2 different conditions among the samples, four statistics (columns) will be reported for each gene/transcript. They are "PPEE", "PPDE", "PostFC" and "RealFC". "PPEE" is the posterior probability (estimated by EBSeq) that a gene/transcript is equally expressed. "PPDE" is the posterior probability that a gene/transcript is differentially expressed. "PostFC" is the posterior fold change (condition 1 over condition2) for a gene/transcript. It is defined as the ratio between posterior mean expression estimates of the gene/transcript for each condition. "RealFC" is the real fold change (condition 1 over condition2) for a gene/transcript.  It is the ratio of the normalized within condition 1 mean count over normalized within condition 2 mean count for the gene/transcript. Fold changes are calculated using EBSeq's 'PostFC' function. The genes/transcripts are reported in descending order of their "PPDE" values.
+
 If there are more than 2 different conditions among the samples, the output format is different. For differential expression analysis with more than 2 conditions, EBSeq will enumerate all possible expression patterns (on which conditions are equally expressed and which conditions are not). Suppose there are k different patterns, the first k columns of the output file give the posterior probability of each expression pattern is true. Patterns are defined in a separate file, 'output_file.pattern'. The k+1 column gives the maximum a posteriori (MAP) expression pattern for each gene/transcript. The k+2 column gives the posterior probability that not all conditions are equally expressed (column name "PPDE"). The genes/transcripts are reported in descending order of their "PPDE" column values. For details on how EBSeq works for more than 2 conditions, please refer to EBSeq's manual.
 
 =item B<output_file.pattern>
 
 This file is only generated when there are more than 2 conditions. It defines all possible expression patterns over the conditions using a matrix with names. Each row of the matrix refers to a different expression pattern and each column gives the expression status of a different condition. Two conditions are equally expressed if and only if their statuses are the same.
 
+=item B<output_file.condmeans>
+
+This file is only generated when there are more than 2 conditions. It gives the normalized mean count value for each gene/transcript at each condition. It is formatted as a matrix with names. Each row represents a gene/transcript and each column represent a condition. The order of genes/transcripts is the same as 'output_file'. This file can be used to calculate fold changes between conditions which users are interested in.  
+
 =back
 
 =head1 EXAMPLES
@@ -107,7 +111,7 @@ The results will be in 'IsoMat.results'.
 
  rsem-run-ebseq GeneMat 3,4,4 GeneMat.results
 
-Two files, 'GeneMat.results' and 'GeneMat.results.pattern', will be generated. 
+Three files, 'GeneMat.results', 'GeneMat.results.pattern', and 'GeneMat.results.condmeans', will be generated. 
 
 =cut