* * *
-<h2 id="introduction">Introduction</h2>
+## <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
addition, it provides posterior mean and 95% credibility interval
estimates for expression levels.
-<h2 id="compilation">Compilation & Installation</h2>
+## <a name="compilation"></a> Compilation & Installation
To compile RSEM, simply run
To take advantage of RSEM's built-in support for the Bowtie alignment
program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
-<h2 id="usage">Usage</h2>
+## <a name="usage"></a> Usage
### I. Preparing Reference Sequences
rsem-prepare-reference --help
to get usage information or visit the [rsem-prepare-reference
-documentation page](rsem-prepare-reference.html).
+documentation page](http://deweylab.biostat.wisc.edu/rsem/rsem-prepare-reference.html).
### II. Calculating Expression Values
rsem-calculate-expression --help
to get usage information or visit the [rsem-calculate-expression
-documentation page](rsem-calculate-expression.html).
+documentation page](http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html).
#### Calculating expression values from single-end data
Refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
-<h2 id="example">Example</h2>
+#### 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,
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
-<h2 id="simulation">Simulation</h2>
+## <a name="simulation"></a> Simulation
### Usage:
output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
-<h2 id="acknowledgements">Acknowledgements</h2>
+## <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.
-<h2 id="license">License</h2>
+## <a name="license"></a> License
RSEM is licensed under the [GNU General Public License v3](http://www.gnu.org/licenses/gpl-3.0.html).