Applications/transabyss - Revision history

Pysdlb: /* Usage */

2022-11-22T10:12:55Z

‎Usage

Pysdlb: /* Navigation */

2022-11-16T11:00:18Z

‎Navigation

Pysdlb at 15:56, 8 November 2022

2022-11-08T15:56:23Z

Pysdlb at 13:11, 13 October 2022

2022-10-13T13:11:11Z

Pysdlb at 13:50, 24 May 2019

2019-05-24T13:50:21Z

Chris.collins: Created page with "TOC ==Application Details== * Description: Trans-ABySS (Assembly By Short Sequences) is a software pipeline written in Python and Perl for analyzing applications/ABySS..."

2017-08-22T21:17:36Z

Created page with "__TOC__ ==Application Details== * Description: Trans-ABySS (Assembly By Short Sequences) is a software pipeline written in Python and Perl for analyzing applications/ABySS..."

New page

__TOC__

==Application Details==

* Description: Trans-ABySS (Assembly By Short Sequences) is a software pipeline written in Python and Perl for analyzing [[applications/ABySS|ABySS]]-assembled transcriptome contigs.
* Version: 1.5.4
* Modules: transabyss/1.5.5
* Licence: BCCA (BC Cancer Agency) academic use

==Usage==
This pipeline can be applied to assemblies generated across a wide range of k values. It first reduces the dataset into smaller sets of non-redundant contigs, and identifies splicing events including exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. The Trans-ABySS algorithms are also able to estimate gene expression levels, identify potential polyadenylation sites, as well as candidate gene-fusion events [https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS]

Because of the nature of such tasks, it may be more appropriate to use [[General/Batch#High_memory_batch_job|highmem]] nodes rather than standard compute nodes.

=== Batch Submission ===
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J transabyss
#SBATCH -N 1
#SBATCH -n 28
#SBATCH -o %N-%j.log
#SBATCH -e %N-%j.err
#SBATCH -p compute
#SBATCH --exclusive

module add transabyss/1.5.5

transabyss --pe R1.fq R2.fq --name transabyss --threads 28 -k 25 --length 200
</pre>

<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
[username@login01 ~]$ sbatch transabyss.job
Submitted batch job 289555
</pre>

==Further Information==

* http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
* http://hpc.mediawiki.hull.ac.uk/Applications/ABySS
* https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS

{|
|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]]
|-
|}

@@ Line 11: / Line 11: @@
 This pipeline can be applied to assemblies generated across a wide range of k values. It first reduces the dataset into smaller sets of non-redundant contigs and identifies splicing events including exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. The Trans-ABySS algorithms are also able to estimate gene expression levels, identify potential polyadenylation sites, as well as candidate gene-fusion events [https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS]
-Because of the nature of such tasks, it may be more appropriate to use [[General/Batch#High_memory_batch_job|highmem]] nodes rather than standard compute nodes.
+Because of the nature of such tasks, it may be more appropriate to use [[FurtherTopics/Advanced_Batch_Jobs#highmem|highmem]] nodes rather than standard compute nodes.
 === Batch Submission ===

← Older revision		Revision as of 11:00, 16 November 2022
Line 40:		Line 40:
	* https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS		* https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS

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

@@ Line 34: / Line 34: @@
 </pre>
-==Further Information==
+==Next Steps==
 * http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

@@ Line 9: / Line 9: @@
 ==Usage==
-This pipeline can be applied to assemblies generated across a wide range of k values. It first reduces the dataset into smaller sets of non-redundant contigs, and identifies splicing events including exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. The Trans-ABySS algorithms are also able to estimate gene expression levels, identify potential polyadenylation sites, as well as candidate gene-fusion events [https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS]
+This pipeline can be applied to assemblies generated across a wide range of k values. It first reduces the dataset into smaller sets of non-redundant contigs and identifies splicing events including exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. The Trans-ABySS algorithms are also able to estimate gene expression levels, identify potential polyadenylation sites, as well as candidate gene-fusion events [https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS]
 Because of the nature of such tasks, it may be more appropriate to use [[General/Batch#High_memory_batch_job|highmem]] nodes rather than standard compute nodes.

@@ Line 40: / Line 40: @@
 * https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS
-{|
+==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]]