Samuel Lampa (UPPMAX): /* Tips and tricks */

2011-09-30T08:43:59Z

‎Tips and tricks

Samuel Lampa (UPPMAX): Created page with "NOTOC {{software info |description=the pipeline stack that comes with the solid sequence platform |license=site license |fields=bioinformatics }} SOLiD [http://solidsoftware..."

2011-09-30T08:43:16Z

Created page with "__NOTOC__ {{software info |description=the pipeline stack that comes with the solid sequence platform |license=site license |fields=bioinformatics }} SOLiD [http://solidsoftware..."

New page

__NOTOC__
{{software info
|description=the pipeline stack that comes with the solid sequence platform
|license=site license
|fields=bioinformatics
}}
SOLiD [http://solidsoftwaretools.com/ {{PAGENAME}}] Bioscope provides a command line for running application-specific sequence analysis tools. The Bioscope framework enables the user to perform off-instrument secondary and tertiary analyses, and it allows configurable bioinformatics workflows for resequencing (mapping, SNP finding (diBayes), copy number variations, inversions, small indels, large indels) and whole transcriptome analysis (mapping, counting, novel transcript finding, UCSC WIG Files creation) Results will be in GFF v3 and SAM formats. The resulting industry-standard files from Bioscope can be used with third-party visualization and analysis software tools.

== Availability ==
{{list resources for software}}

== Tips and tricks ==
On UPPMAX/UPPNEX you find bioscope in the module systems on the Kalkyl cluster.

Please type :
module load bioinfo-tools bioscope
To load the module. the command is then
bioscope.sh -A b2010999
To run on Kalkyl you need to specify what project shall be accounted for your job run.
Bioscope integrates to the SLURM queueing system there so you only need to start bioscope.sh on a login node.
We recommend you run it in the background by using "noup"
nohup ./run.sh MatoBam_nohup.out
Where run.sh have the run line bioscope.sh -A b2010999 -l MaToBam.log MaToBam.plan

Nohup will run the job in the background and you can monitor the progress by reading the MatoBam_nohup.out.

Bioscope can today use at the most 11 nodes for one bioscope run, and you can at the most start two parallel runs. This is due to the limit in the SLURM system. If you need to run several different bioscope runs. I recommend you running them one after another.

Find attached the user manual to this post you need to be loged in on a registered account to read the attachment..

You can also find some test data on the system under the folder:

/bubo/nobackup/uppnex/bioscopedata

== License ==
{{show license}}

== Experts ==
{{list experts}}

== Links ==
* [http://solidsoftwaretools.com/ Official website]

@@ Line 11: / Line 11: @@
 == Tips and tricks ==
-On UPPMAX/UPPNEX you find bioscope in the module systems on the Kalkyl cluster.
+On UPPMAX/[https://www.uppnex.uu.se UPPNEX] you find bioscope in the module systems on the Kalkyl cluster.
 Please type :

Bioscope - Revision history

Samuel Lampa (UPPMAX): /* Tips and tricks */

Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=the pipeline stack that comes with the solid sequence platform |license=site license |fields=bioinformatics }} SOLiD [http://solidsoftware..."

Samuel Lampa (UPPMAX): Created page with "NOTOC {{software info |description=the pipeline stack that comes with the solid sequence platform |license=site license |fields=bioinformatics }} SOLiD [http://solidsoftware..."