X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-run-ebseq;h=cd4750f4a6107dccbdb27efbaf6e56e025d0a2ae;hb=3c03759b005d7ca39d65ddf996d8e440ab5aabb6;hp=c4140c53551f6be26ad23435194edff2dd609cc5;hpb=80182d3120cde6e3831fc3ea99af91f20dade08b;p=rsem.git

diff --git a/rsem-run-ebseq b/rsem-run-ebseq
index c4140c5..cd4750f 100755
--- a/rsem-run-ebseq
+++ b/rsem-run-ebseq
@@ -93,6 +93,10 @@ If there are more than 2 different conditions among the samples, the output form
 
 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