README.md is updated

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 5c6943bd42f32d5631228267cd19aa1cffd2d2ec..725d1cb9c0cc1481a0c0725ee327508d27c6565c 100644 (file)
--- a/README.md
+++ b/README.md
@@ -46,6 +46,13 @@ To compile RSEM, simply run
    
     make
 
+For cygwin users, please uncomment the 3rd and 7th line in
+'sam/Makefile' before you run 'make'.
+
+To compile EBSeq, which is included in the RSEM package, run
+
+    make ebseq
+
 To install, simply put the rsem directory in your environment's PATH
 variable.
 
@@ -279,7 +286,7 @@ to get usage information or read the following subsections.
 
 __reference_name:__ The name of RSEM references, which should be already generated by 'rsem-prepare-reference'              
 
-__estimated_model_file:__ This file describes how the RNA-Seq reads will be sequenced given the expression levels. It determines what kind of reads will be simulated (single-end/paired-end, w/o quality score) and includes parameters for fragment length distribution, read start position distribution, sequencing error models, etc. Normally, this file should be learned from real data using 'rsem-calculate-expression'. The file can be found under the 'sample_name.stat' folder with the name of 'sample_name.model'    
+__estimated_model_file:__ This file describes how the RNA-Seq reads will be sequenced given the expression levels. It determines what kind of reads will be simulated (single-end/paired-end, w/o quality score) and includes parameters for fragment length distribution, read start position distribution, sequencing error models, etc. Normally, this file should be learned from real data using 'rsem-calculate-expression'. The file can be found under the 'sample_name.stat' folder with the name of 'sample_name.model'. 'model_file_description.txt' provides the format and meanings of this file.    
 
 __estimated_isoform_results:__ This file contains expression levels for all isoforms recorded in the reference. It can be learned using 'rsem-calculate-expression' from real data. The corresponding file users want to use is 'sample_name.isoforms.results'. If simulating from user-designed expression profile is desired, start from a learned 'sample_name.isoforms.results' file and only modify the 'TPM' column. The simulator only reads the TPM column. But keeping the file format the same is required.