Pysdlb at 11:45, 15 November 2022

2022-11-15T11:45:33Z

Pysdlb: Pysdlb moved page Rsem to Applications/Rsem without leaving a redirect

2017-04-19T10:38:38Z

Pysdlb moved page Rsem to Applications/Rsem without leaving a redirect

Pysdlb: Created page with "TOC ==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...."

2017-04-19T10:28:46Z

Created page with "__TOC__ ==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...."

New page

__TOC__

==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/]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

← Older revision		Revision as of 11:45, 15 November 2022
Line 39:		Line 39:


−	==~~Further Information~~==	+	==Next Steps==

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

← Older revision	Revision as of 10:38, 19 April 2017
(No difference)

Applications/Rsem - Revision history

Pysdlb at 11:45, 15 November 2022

Pysdlb: Pysdlb moved page Rsem to Applications/Rsem without leaving a redirect

Pysdlb: Created page with "__TOC__ ==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...."

Pysdlb: Created page with "TOC ==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...."