v1.1.2

diff --git a/README.txt b/README.txt
index 3ef2603e9273c8c163b90c47870fcc2813eb0642..0a76a6f06ab54afb865619ae30dafb464e2b1e89 100644 (file)
--- a/README.txt
+++ b/README.txt
@@ -66,7 +66,7 @@ documentation page](rsem-prepare-reference.html).
 
 ### II. Calculating Expression Values
 
-To prepare the reference sequences, you should run the
+To calculate expression values, you should run the
 'rsem-calculate-expression' program.  Run 
 
     rsem-calculate-expression --help
@@ -74,10 +74,6 @@ To prepare the reference sequences, you should run the
 to get usage information or visit the [rsem-calculate-expression
 documentation page](rsem-calculate-expression.html).
 
-Note: RSEM no longer provides nu values. Instead, RSEM provides
-nrf(normalized read fraction), which is a normalized version of theta
-vector excluding theta_0.
-
 #### Calculating expression values from single-end data
 
 For single-end models, users have the option of providing a fragment

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 3539fa498e76e4c902caa87fdb242433207f65ae..de412ae8227e5427ced5b5bb78883cd863a8adad 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -396,7 +396,7 @@ Comma-separated list of files containing downstream reads which are paired with
 
 =item B<input>
 
-SAM/BAM formatted input file.  If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. SAM/BAM format used is SAM Spec v1.2. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements.
+SAM/BAM formatted input file.  If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements.
 
 =item B<reference_name>                        
 
@@ -538,7 +538,7 @@ One simple way to make the alignment file (e.g. input.sam) satisfying RSEM's req
 
   sort -k 1,1 -s input.sam > input.sorted.sam
 
-The SAM/BAM format RSEM uses is v1.2.
+The SAM/BAM format RSEM uses is v1.3. However, it is compatible with old SAM/BAM format. 
 
 The user must run 'rsem-prepare-reference' with the appropriate reference before using this program.