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* [[Estimating Gene Count Exercise]] | * [[Estimating Gene Count Exercise]] | ||
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* [[Differential Expression]] | * [[Differential Expression]] | ||
* [[Differential Expression Exercise]] | * [[Differential Expression Exercise]] | ||
Revision as of 22:15, 8 April 2017
Contents
Usage of Cluster
Documented Programs
The following can be seen as extra notes referring to these programs usage on the marvin cluster, with an emphais on example use-cases. Most, if not all, will have their own special websites, with more detailed manuals and further information.
| * abacas | * albacore | * ariba | * assembly-stats | * augustus | * BamQC |
| * bcftools | * bedtools | * BLAST | * blast2go: b2g4pipe | * bowtie | * bowtie2 |
| * bwa | * BUSCO | * CAFE | * canu | * cd-hit | * cegma |
| * clustal | * cramtools | * detonate | * diamond | * ensembl | * ETE |
| * FASTQC and MultiQC | * Archaeopteryx and Forester | * GapFiller | * GenomeTools | * gubbins | * JBrowse |
| * kallisto | * last | * lastz | * Mash | * mega | * MUMmer |
| * NanoSim | * OrthoFinder | * quast | * PGAP | * picard-tools | * poRe |
| * poretools | * prokka | * pyrad | * python | * R | * RAxML |
| * Repeatmasker | * rnammer | * roary | * RSeQC | * samtools | * Satsuma |
| * sickle | * SPAdes | * sra-tools | * srst2 | * SSPACE | * stacks |
| * trimmomatic | * Trinity | * t-coffee | * velvet |
Queue Manager Tips
A cluster is a shared resource with different users running different types of analyses. Nearly all clusters use a piece of software called a queue manager to fairly share out the resource. The queue manager on marvin is called Grid Engine, and it has several commands available, all beginning with q and with qsub being the most commonly used as it submits a command via a jobscript to be processed. Here are some tips:
Data Examples
Procedures
(short sequence of tasks with a certain short-term goal, often, a simple script)
Explanations
Pipelines
(Workflow with a specific end-goal)
- Trinity_Protocol
- STAR BEAST
- callSNPs.py
- mapping.py
- Edgen RNAseq
- Miseq Prokaryote FASTQ analysis
- snpcallphylo
- Bottlenose dolphin population genomic analysis
Protocols
(Extensive workflows with different with several possible end goals)
Cluster Administration
- Hardware Issues
- Admin Tips
- RedHat
- Globus_gridftp
- Galaxy Setup
- Son of Gridengine
- Blas Libraries
- CMake
- Users and Groups
- emailing
- biotime machine
- node1 issues
- 6TB storage expansion
- Home directories max-out incident 28.11.2016
- Frontend Restart
- environment-modules
- H: drive on cluster
- Incident: Can't connect to BerkeleyDB
- Bioinformatics Wordpress Site
- Backups
- Python DRMAA
- SAN disconnect incident 10.01.2017
- Memory repair glitch 16.02.2017
- node9 network failure incident 16-20.03.2017
Courses
I2U4BGA
- Original schedule
- New schedule
- Actual schedule
- Course itself
- Directory Organization Exercise
- Glossary
- Key Bindings
- one-liners
- Cheatsheets
- Links
- pandoc modified manual
RNAseq for DGE
- Theoretical background
- Estimating Gene Count
- Estimating Gene Count Exercise
- Differential Expression
- Differential Expression Exercise
- Functional Analysis
- Functional Analysis Exercise
