Style edits to rsem-plot-model

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 0f4d9826f5fe850c6d7c9329bf9f8ef0fed4d167..f8c4e2709436f97e446ac3dbbda2306818df70f4 100644 (file)
--- a/README.md
+++ b/README.md
@@ -27,7 +27,7 @@ the EM algorithm, single-end and paired-end read data, quality scores,
 variable-length reads and RSPD estimation. It can also generate
 genomic-coordinate BAM files and UCSC wiggle files for visualization. In
 addition, it provides posterior mean and 95% credibility interval
-estimates for expression levels.
+estimates for expression levels. 
 
 ## <a name="compilation"></a> Compilation & Installation
 
@@ -40,9 +40,13 @@ variable.
 
 ### Prerequisites
 
+C++ and Perl are required to be installed. 
+
 To take advantage of RSEM's built-in support for the Bowtie alignment
 program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
 
+If you want to plot model learned by RSEM, you should also install R. 
+
 ## <a name="usage"></a> Usage
 
 ### I. Preparing Reference Sequences
@@ -96,6 +100,12 @@ and provide the SAM or BAM file as an argument.  When using an
 alternative aligner, you may also want to provide the --no-bowtie option
 to rsem-prepare-reference so that the Bowtie indices are not built.
 
+However, please note that RSEM does ** not ** support gapped
+alignments. So make sure that your aligner does not produce alignments
+with intersions/deletions. Also, please make sure that you use
+'reference_name.idx.fa' , which is generated by RSEM, to build your
+aligner's indices.
+
 ### III. Visualization
 
 RSEM contains a version of samtools in the 'sam' subdirectory. When
@@ -123,6 +133,34 @@ 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).
 
+#### c) Visualize the model learned by RSEM
+
+RSEM provides an R script, 'rsem-plot-model', for visulazing the model learned.
+
+Usage:
+    
+    rsem-plot-model sample_name outF
+
+sample_name: the name of the sample analyzed    
+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 observed
+quality given a reference base, position vs percentage of sequencing
+error given a reference base and histogram of reads with different
+number of alignments.
+
+fragment length distribution and mate length distribution: x-axis is fragment/mate length, y axis is the probability of generating a fragment/mate with the associated length
+
+RSPD: Read Start Position Distribution. x-axis is bin number, y-axis is the probability of each bin. RSPD can be used as an indicator of 3' bias
+
+Quality score vs. observed quality given a reference base: x-axis is Phred quality scores associated with data, y-axis is the "observed quality", Phred quality scores learned by RSEM from the data. Q = -10log_10(P), where Q is Phred quality score and P is the probability of sequencing error for a particular base
+
+Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
+
+Histogram of reads with different number of alignments: x-axis is the number of alignments a read has and y-axis is the number of such reads. The inf in x-axis means number of reads filtered due to too many alignments
+ 
 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will
@@ -170,9 +208,7 @@ output_name.sim.isoforms.results, output_name.sim.genes.results : Results estima
 
 ## <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
+RSEM uses the [Boost C++](http://www.boost.org) and
 [samtools](http://samtools.sourceforge.net) libraries.
 
 ## <a name="license"></a> License