Fixed bugs in the Gibbs sampler. Fixed a bug which will set probF to 0 if the protoco...

[rsem.git] / README.md

diff --git a/README.md b/README.md
index b7a5204d1f904937deb5fb30c6b2ee1463bb8136..b95c4ea51cffc471d5b211ab84fc07aabeeb0e64 100644 (file)
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@ Table of Contents
 
 * * *
 
-## Introduction <a name="introduction"></a>
+## <a name="introduction"></a> Introduction
 
 RSEM is a software package for estimating gene and isoform expression
 levels from RNA-Seq data.  The new RSEM package (rsem-1.x) provides an
@@ -29,7 +29,7 @@ genomic-coordinate BAM files and UCSC wiggle files for visualization. In
 addition, it provides posterior mean and 95% credibility interval
 estimates for expression levels.
 
-## Compilation & Installation <a name="compilation"></a>
+## <a name="compilation"></a> Compilation & Installation
 
 To compile RSEM, simply run
    
@@ -43,7 +43,7 @@ variable.
 To take advantage of RSEM's built-in support for the Bowtie alignment
 program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
 
-## Usage <a name="usage"></a>
+## <a name="usage"></a> Usage
 
 ### I. Preparing Reference Sequences
 
@@ -123,7 +123,24 @@ wiggle_name: the name the user wants to use for this wiggle plot
 
 Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
 
-## Example <a name="example"></a>
+#### c) Visualize the model learned by RSEM
+
+RSEM provides an R script, 'rsem-plot-model', for visulazing the model learned.
+
+Usage:
+    
+    rsem-plot-model modelF outF
+
+modelF: the sample_name.model file generated by RSEM    
+outF: the file name for plots generated from the model. It is a pdf file    
+
+The plots generated depends on read type and user configuration. It
+may include fragment length distribution, mate length distribution,
+read start position distribution (RSPD), quality score vs percentage
+of sequecing error given the reference base, position vs percentage of
+sequencing error given the reference base.
+
+## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will
 use a reference_name of 'mm9'.  We have a FASTQ-formatted file,
@@ -143,7 +160,7 @@ The commands for this scenario are as follows:
     rsem-calculate-expression --bowtie-path /sw/bowtie --phred64-quals --fragment-length-mean 150.0 --fragment-length-sd 35.0 -p 8 --out-bam --calc-ci --memory-allocate 1024 /data/mmliver.fq /ref/mm9 mmliver_single_quals
     rsem-bam2wig mmliver_single_quals.sorted.bam mmliver_single_quals.sorted.wig mmliver_single_quals
 
-## Simulation <a name="simulation"></a>
+## <a name="simulation"></a> Simulation
 
 ### Usage: 
 
@@ -168,13 +185,13 @@ output_name_1.fq & output_name_2.fq if paired-end with quality score.
 
 output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
 
-## Acknowledgements <a name="acknowledgements"></a> 
+## <a name="acknowledgements"></a> Acknowledgements
 
 RSEM uses randomc.h and mersenne.cpp from
 <http://lxnt.info/rng/randomc.htm> for random number generation. RSEM
 also uses the [Boost C++](http://www.boost.org) and
 [samtools](http://samtools.sourceforge.net) libraries.
 
-## License <a name="license"></a>
+## <a name="license"></a> License
 
 RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).