* [Usage](#usage)
* [Example](#example)
* [Simulation](#simulation)
+* [Generate Transcript-to-Gene-Map from Trinity Output](#gen_trinity)
* [Acknowledgements](#acknowledgements)
* [License](#license)
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 read alignments.
+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
Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
-Histogram of read alignments: x-axis is the number of alignments a read has and y-axis is the number of such reads
+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
rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]
-estimated_model_file: File containing model parameters. Generated by
+estimated_model_file: file containing model parameters. Generated by
rsem-calculate-expression.
-estimated_isoform_results: File containing isoform expression levels.
+estimated_isoform_results: file containing isoform expression levels.
Generated by rsem-calculate-expression.
theta0: fraction of reads that are "noise" (not derived from a transcript).
N: number of reads to simulate.
output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
+## <a name="gen_trinity"></a> Generate Transcript-to-Gene-Map from Trinity Output
+
+For Trinity users, RSEM provides a perl script to generate transcript-to-gene-map file from the fasta file produced by Trinity.
+
+### Usage:
+
+ extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
+
+trinity_fasta_file: the fasta file produced by trinity, which contains all transcripts assembled.
+map_file: transcript-to-gene-map file's name.
+
## <a name="acknowledgements"></a> Acknowledgements
RSEM uses the [Boost C++](http://www.boost.org) and