Difference between revisions of "Main Page"
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Line 12: | Line 12: | ||
|* [[albacore]] | |* [[albacore]] | ||
|* [[ariba]] | |* [[ariba]] | ||
+ | |* [[aspera]] | ||
|* [[assembly-stats]] | |* [[assembly-stats]] | ||
|* [[augustus]] | |* [[augustus]] | ||
+ | |- | ||
|* [[BamQC]] | |* [[BamQC]] | ||
− | | | + | |* [[bamtools]] |
+ | |* [[banjo]] | ||
|* [[bcftools]] | |* [[bcftools]] | ||
|* [[bedtools]] | |* [[bedtools]] | ||
+ | |* [[bgenie]] | ||
+ | |- | ||
|* [[BLAST]] | |* [[BLAST]] | ||
+ | |* [[Blat]] | ||
|* [[blast2go: b2g4pipe]] | |* [[blast2go: b2g4pipe]] | ||
|* [[bowtie]] | |* [[bowtie]] | ||
|* [[bowtie2]] | |* [[bowtie2]] | ||
+ | |* [[bwa]] | ||
|- | |- | ||
− | |||
|* [[BUSCO]] | |* [[BUSCO]] | ||
|* [[CAFE]] | |* [[CAFE]] | ||
Line 29: | Line 35: | ||
|* [[cd-hit]] | |* [[cd-hit]] | ||
|* [[cegma]] | |* [[cegma]] | ||
+ | |* [[clustal]] | ||
|- | |- | ||
− | |||
|* [[cramtools]] | |* [[cramtools]] | ||
+ | |* [[deeptools]] | ||
|* [[detonate]] | |* [[detonate]] | ||
|* [[diamond]] | |* [[diamond]] | ||
+ | |* [[ea-utils]] | ||
|* [[ensembl]] | |* [[ensembl]] | ||
+ | |- | ||
|* [[ETE]] | |* [[ETE]] | ||
− | |||
|* [[FASTQC and MultiQC]] | |* [[FASTQC and MultiQC]] | ||
|* [[Archaeopteryx and Forester]] | |* [[Archaeopteryx and Forester]] | ||
Line 42: | Line 50: | ||
|* [[GenomeTools]] | |* [[GenomeTools]] | ||
|* [[gubbins]] | |* [[gubbins]] | ||
+ | |- | ||
|* [[JBrowse]] | |* [[JBrowse]] | ||
− | |||
|* [[kallisto]] | |* [[kallisto]] | ||
+ | |* [[kentUtils]] | ||
|* [[last]] | |* [[last]] | ||
|* [[lastz]] | |* [[lastz]] | ||
+ | |* [[macs2]] | ||
+ | |- | ||
|* [[Mash]] | |* [[Mash]] | ||
|* [[mega]] | |* [[mega]] | ||
+ | |* [[meryl]] | ||
|* [[MUMmer]] | |* [[MUMmer]] | ||
+ | |* [[NanoSim]] | ||
+ | |* [[nseq]] | ||
|- | |- | ||
− | |||
|* [[OrthoFinder]] | |* [[OrthoFinder]] | ||
− | |* [[ | + | |* [[PASA]] |
+ | |* [[perl]] | ||
|* [[PGAP]] | |* [[PGAP]] | ||
|* [[picard-tools]] | |* [[picard-tools]] | ||
Line 62: | Line 76: | ||
|* [[pyrad]] | |* [[pyrad]] | ||
|* [[python]] | |* [[python]] | ||
+ | |* [[qualimap]] | ||
+ | |* [[quast]] | ||
+ | |- | ||
+ | |* [[qiime2]] | ||
|* [[R]] | |* [[R]] | ||
|* [[RAxML]] | |* [[RAxML]] | ||
− | |||
|* [[Repeatmasker]] | |* [[Repeatmasker]] | ||
+ | |* [[Repeatmodeler]] | ||
|* [[rnammer]] | |* [[rnammer]] | ||
+ | |- | ||
|* [[roary]] | |* [[roary]] | ||
|* [[RSeQC]] | |* [[RSeQC]] | ||
|* [[samtools]] | |* [[samtools]] | ||
|* [[Satsuma]] | |* [[Satsuma]] | ||
− | |||
|* [[sickle]] | |* [[sickle]] | ||
|* [[SPAdes]] | |* [[SPAdes]] | ||
+ | |- | ||
+ | |* [[squid]] | ||
|* [[sra-tools]] | |* [[sra-tools]] | ||
|* [[srst2]] | |* [[srst2]] | ||
|* [[SSPACE]] | |* [[SSPACE]] | ||
|* [[stacks]] | |* [[stacks]] | ||
+ | |* [[Thor]] | ||
|- | |- | ||
+ | |* [[Tophat]] | ||
|* [[trimmomatic]] | |* [[trimmomatic]] | ||
|* [[Trinity]] | |* [[Trinity]] | ||
|* [[t-coffee]] | |* [[t-coffee]] | ||
+ | |* [[Unicycler]] | ||
|* [[velvet]] | |* [[velvet]] | ||
+ | |- | ||
+ | |* [[ViennaRNA]] | ||
|} | |} | ||
Line 102: | Line 127: | ||
* [[Patric]] | * [[Patric]] | ||
* [[NCBI]] | * [[NCBI]] | ||
+ | * [[IGSR/1000 Genomes]] | ||
= Explanations= | = Explanations= | ||
* [[ITUcourse]] | * [[ITUcourse]] | ||
* [[VCF]] | * [[VCF]] | ||
+ | * [[Maximum Likelihood]] | ||
+ | * [[SNP Analysis and phylogenetics]] | ||
+ | * [[Normalization]] | ||
= Pipelines = | = Pipelines = | ||
− | (Workflow with | + | (Workflow with specific end-goals) |
* [[Trinity_Protocol]] | * [[Trinity_Protocol]] | ||
* [[STAR BEAST]] | * [[STAR BEAST]] | ||
* [[callSNPs.py]] | * [[callSNPs.py]] | ||
+ | * [[pairwiseCallSNPs]] | ||
* [[mapping.py]] | * [[mapping.py]] | ||
* [[Edgen RNAseq]] | * [[Edgen RNAseq]] | ||
Line 117: | Line 147: | ||
* [[snpcallphylo]] | * [[snpcallphylo]] | ||
* [[Bottlenose dolphin population genomic analysis]] | * [[Bottlenose dolphin population genomic analysis]] | ||
+ | * [[ChIP-Seq Top2 in Yeast]] | ||
+ | * [[ChIP-Seq Top2 in Yeast 12.09.2017]] | ||
+ | * [[ChIP-Seq Top2 in Yeast 07.11.2017]] | ||
+ | * [[Bisulfite Sequencing]] | ||
+ | * [[microRNA and Salmo Salar]] | ||
=Protocols= | =Protocols= | ||
Line 123: | Line 158: | ||
* [[MinION (Oxford Nanopore)]] | * [[MinION (Oxford Nanopore)]] | ||
* [[MinKNOW folders and log files]] | * [[MinKNOW folders and log files]] | ||
+ | * [[Research Data Management]] | ||
+ | * [[MicroRNAs]] | ||
+ | |||
+ | = Tech Reviews = | ||
+ | * [[SWATH-MS Data Analysis]] | ||
= Cluster Administration = | = Cluster Administration = | ||
* [[Hardware Issues]] | * [[Hardware Issues]] | ||
+ | * [[marvin and IPMI (remote hardware control)]] | ||
* [[Admin Tips]] | * [[Admin Tips]] | ||
* [[RedHat]] | * [[RedHat]] | ||
Line 134: | Line 175: | ||
* [[CMake]] | * [[CMake]] | ||
* [[Users and Groups]] | * [[Users and Groups]] | ||
+ | * [[Installing software on marvin]] | ||
* [[emailing]] | * [[emailing]] | ||
* [[biotime machine]] | * [[biotime machine]] | ||
+ | * [[SCAN-pc laptop]] | ||
* [[node1 issues]] | * [[node1 issues]] | ||
* [[6TB storage expansion]] | * [[6TB storage expansion]] | ||
+ | * [[SAN relocation task]] | ||
* [[Home directories max-out incident 28.11.2016]] | * [[Home directories max-out incident 28.11.2016]] | ||
* [[Frontend Restart]] | * [[Frontend Restart]] | ||
Line 149: | Line 193: | ||
* [[Memory repair glitch 16.02.2017]] | * [[Memory repair glitch 16.02.2017]] | ||
* [[node9 network failure incident 16-20.03.2017]] | * [[node9 network failure incident 16-20.03.2017]] | ||
+ | * [[Incorrect rebooting of marvin 19.09.2017]] | ||
= Courses = | = Courses = | ||
Line 157: | Line 202: | ||
* [[Actual schedule]] | * [[Actual schedule]] | ||
* [[Course itself]] | * [[Course itself]] | ||
− | * [[Biolinux Source | + | * [[Biolinux Source course]] |
* [[Directory Organization Exercise]] | * [[Directory Organization Exercise]] | ||
* [[Glossary]] | * [[Glossary]] | ||
Line 165: | Line 210: | ||
* [[Links]] | * [[Links]] | ||
* [[pandoc modified manual]] | * [[pandoc modified manual]] | ||
+ | * [[Command Line Exercises]] | ||
= hdi2u = | = hdi2u = | ||
Line 171: | Line 217: | ||
* [[hdi2u_intro]] | * [[hdi2u_intro]] | ||
− | * [[ | + | * [[hdi2u_commandbased_exercises]] |
− | * [[ | + | * [[hdi2u_dirorg_exercise]] |
− | * [[ | + | * [[hdi2u_rendertotsv_exercise]] |
− | |||
= RNAseq for DGE = | = RNAseq for DGE = | ||
Line 185: | Line 230: | ||
* [[Differential Expression Exercise]] | * [[Differential Expression Exercise]] | ||
* [[Functional Analysis Exercise]] | * [[Functional Analysis Exercise]] | ||
+ | |||
+ | = Introduction to Unix 2017 = | ||
+ | * [[Introduction_to_Unix_2017]] | ||
Revision as of 13:36, 2 February 2018
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 | * aspera | * assembly-stats | * augustus |
* BamQC | * bamtools | * banjo | * bcftools | * bedtools | * bgenie |
* BLAST | * Blat | * blast2go: b2g4pipe | * bowtie | * bowtie2 | * bwa |
* BUSCO | * CAFE | * canu | * cd-hit | * cegma | * clustal |
* cramtools | * deeptools | * detonate | * diamond | * ea-utils | * ensembl |
* ETE | * FASTQC and MultiQC | * Archaeopteryx and Forester | * GapFiller | * GenomeTools | * gubbins |
* JBrowse | * kallisto | * kentUtils | * last | * lastz | * macs2 |
* Mash | * mega | * meryl | * MUMmer | * NanoSim | * nseq |
* OrthoFinder | * PASA | * perl | * PGAP | * picard-tools | * poRe |
* poretools | * prokka | * pyrad | * python | * qualimap | * quast |
* qiime2 | * R | * RAxML | * Repeatmasker | * Repeatmodeler | * rnammer |
* roary | * RSeQC | * samtools | * Satsuma | * sickle | * SPAdes |
* squid | * sra-tools | * srst2 | * SSPACE | * stacks | * Thor |
* Tophat | * trimmomatic | * Trinity | * t-coffee | * Unicycler | * velvet |
* ViennaRNA |
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 specific end-goals)
- Trinity_Protocol
- STAR BEAST
- callSNPs.py
- pairwiseCallSNPs
- mapping.py
- Edgen RNAseq
- Miseq Prokaryote FASTQ analysis
- snpcallphylo
- Bottlenose dolphin population genomic analysis
- ChIP-Seq Top2 in Yeast
- ChIP-Seq Top2 in Yeast 12.09.2017
- ChIP-Seq Top2 in Yeast 07.11.2017
- Bisulfite Sequencing
- microRNA and Salmo Salar
Protocols
(Extensive workflows with different with several possible end goals)
- Synthetic Long reads
- MinION (Oxford Nanopore)
- MinKNOW folders and log files
- Research Data Management
- MicroRNAs
Tech Reviews
Cluster Administration
- Hardware Issues
- marvin and IPMI (remote hardware control)
- Admin Tips
- RedHat
- Globus_gridftp
- Galaxy Setup
- Son of Gridengine
- Blas Libraries
- CMake
- Users and Groups
- Installing software on marvin
- emailing
- biotime machine
- SCAN-pc laptop
- node1 issues
- 6TB storage expansion
- SAN relocation task
- 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
- Incorrect rebooting of marvin 19.09.2017
Courses
I2U4BGA
- Original schedule
- New schedule
- Actual schedule
- Course itself
- Biolinux Source course
- Directory Organization Exercise
- Glossary
- Key Bindings
- one-liners
- Cheatsheets
- Links
- pandoc modified manual
- Command Line Exercises
hdi2u
The half-day linux course held on 20th April. Modified version of I2U4BGA.
RNAseq for DGE
- Theoretical background
- Quality Control and Preprocessing
- Mapping to Reference
- Mapping Quality Exercise
- Key Aspects of using R
- Estimating Gene Count Exercise
- Differential Expression Exercise
- Functional Analysis Exercise
Introduction to Unix 2017