X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=f8c4e2709436f97e446ac3dbbda2306818df70f4;hb=481f6cdebcae92c5ce2cf71d4f5b103565b05e44;hp=0f4d9826f5fe850c6d7c9329bf9f8ef0fed4d167;hpb=1d2a4ae0eae7f727daa6f7565bf5075645fe2add;p=rsem.git
diff --git a/README.md b/README.md
index 0f4d982..f8c4e27 100644
--- 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.
## 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.
+
## 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
+
## 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
## Acknowledgements
-RSEM uses randomc.h and mersenne.cpp from
- 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.
## License