View source for Applications/Rsem

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==Application Details==

* Description: RSEM can extract reference transcripts from a genome if you provide it with gene annotations in a GTF/GFF3 file
* Version:1.3.0
* Modules: rsem/1.3.0
* Licence: GNU General Public License v3.

==Usage==

Prior-enhanced RSEM (pRSEM) uses complementary information (e.g. ChIP-seq data) to allocate RNA-seq multi-mapping fragments. We included pRSEM code in the subfolder pRSEM/ as well as in RSEM’s scripts rsem-prepare-reference and rsem-calculate-expression. 

===Simulation===

RSEM provides users the rsem-simulate-reads program to simulate RNA-Seq data based on parameters learned from real data sets. Run

'''rsem-simulate-reads'''

to get usage information or read the following subsections.


<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]
</pre>



===Example===

Suppose we want to simulate 50 millon single-end reads with quality scores and use the parameters learned from Example. In addition, we set theta0 as 0.2 and output_name as simulated_reads. The command is:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

[username@login]$ module add rsem/1.3.0
[username@login]$ rsem-simulate-reads /ref/mouse_0 mmliver_single_quals.stat/mmliver_single_quals.model mmliver_single_quals.isoforms.results 0.2 50000000 simulated_reads 

</pre>


==Further Information==

* [https://deweylab.github.io/RSEM/ https://deweylab.github.io/RSEM/]

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