Applications/Transrate - Revision history

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2022-11-16T11:00:30Z

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Pysdlb at 11:41, 15 November 2022

2022-11-15T11:41:54Z

Pysdlb at 12:56, 13 October 2022

2022-10-13T12:56:51Z

Pysdlb at 13:49, 24 May 2019

2019-05-24T13:49:49Z

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

2017-04-19T13:36:25Z

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

Pysdlb at 13:33, 19 April 2017

2017-04-19T13:33:38Z

Pysdlb: Created page with "TOC ==Application Details== * Description: Transrate is software for de-novo transcriptome assembly quality analysis. * Version: 1.0.3 * Modules: transrate/1.0.3 * Licen..."

2017-04-19T13:32:38Z

Created page with "__TOC__ ==Application Details== * Description: Transrate is software for de-novo transcriptome assembly quality analysis. * Version: 1.0.3 * Modules: transrate/1.0.3 * Licen..."

New page

__TOC__

==Application Details==

* Description: Transrate is software for de-novo transcriptome assembly quality analysis.
* Version: 1.0.3
* Modules: transrate/1.0.3
* Licence: Free, open-source

==Usage==

Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.

===Example===

You can examine your contigs without using the reads or a reference. All you need is the assembly in FASTA format.

For example if you have the assembly in the file '''transcripts.fa''':

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

[username@login]$ module add transrate/1.0.3
[username@login]$ transrate --assembly transcripts.fa

</pre>

==Further Information==

* [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html]

{|
|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 11:00, 16 November 2022
Line 29:		Line 29:
	* [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html]		* [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

← Older revision		Revision as of 11:41, 15 November 2022
Line 25:		Line 25:


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

	* [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html]		* [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html]

@@ Line 10: / Line 10: @@
 ==Usage==
-Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.
+Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, and reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.
 ===Example===
@@ Line 16: / Line 16: @@
 You can examine your contigs without using the reads or a reference. All you need is the assembly in FASTA format.
-For example if you have the assembly in the file '''transcripts.fa''':
+For example, if you have the assembly in the file '''transcripts.fa''':
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

@@ Line 29: / Line 29: @@
 * [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

← Older revision	Revision as of 13:36, 19 April 2017
(No difference)

@@ Line 18: / Line 18: @@
 For example if you have the assembly in the file '''transcripts.fa''':
-<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
+<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@login]$ module add transrate/1.0.3
 [username@login]$ transrate --assembly transcripts.fa
 </pre>