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start [2024/09/13 10:01] – 134.190.251.141start [2026/03/09 13:08] (current) – [Protein structure prediction] 172.20.112.81
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 [[ RAM and ROM|RAM and CPU memory - Perun Queues ]] [[ RAM and ROM|RAM and CPU memory - Perun Queues ]]
 +
 +[[ GPU nodes and how to work with them|GPU nodes and how to work with them ]]
  
 [[ Perun and Environments|Perun and Environments ]] [[ Perun and Environments|Perun and Environments ]]
 +
 +[[ Perun and Custom Environments|Perun and Custom Environments ]]
  
 [[ GitHub repositories of the lab|GitHub repositories of the lab ]] [[ GitHub repositories of the lab|GitHub repositories of the lab ]]
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 ==== Bioconda ==== ==== Bioconda ====
  
-====Tips and Tricks====+[[ Making Bioconda recipes|Making Bioconda recipes ]] 
 + 
 +===Tips and Tricks===
  
 The idea of this section is to share command line tips and tricks that you have found made it a lot easier to do bioinformatics work. This can range from basic UNIX things like setting up your terminal environment, configuring your SSH connections or managing your filesystem to explaining new bioinformatics tools and how to work with large scale computer clusters. The idea of this section is to share command line tips and tricks that you have found made it a lot easier to do bioinformatics work. This can range from basic UNIX things like setting up your terminal environment, configuring your SSH connections or managing your filesystem to explaining new bioinformatics tools and how to work with large scale computer clusters.
  
 Recordings of the **Tips and Tricks** meetings are available for downloading or viewing online  [[https://perun.biochem.dal.ca/downloads/icgvideo/TAT/|here]] Recordings of the **Tips and Tricks** meetings are available for downloading or viewing online  [[https://perun.biochem.dal.ca/downloads/icgvideo/TAT/|here]]
 +
 +Or directly on Perun, on ''/scratch3/downloads/icgvideo/TAT''
 +
  
 ===The Terminal=== ===The Terminal===
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 ====Gene Prediction==== ====Gene Prediction====
  
-[[gene_prediction_just_genemark| Gene prediction with just GeneMark]]+[[gene_prediction_just_genemark|[Ab initio] Gene prediction with just GeneMark]]
  
-[[gene_prediction_with_braker2_pipeline|Gene prediction with Braker2 pipeline]]+[[gene_prediction_just_augustus|[Ab initio] Gene prediction with just Augustus]]
  
-[[gene_prediction_with_funannotate| Gene prediction with the Funannotate pipeline]]+[[gene_prediction_find_supported_orfs|[RNAseq-informed] Gene prediction with find_supported_orfs.py]]
  
-[[automatically_fixing_gene_models| Improving gene models with fix_genes_with_false_introns.py]]+[[gene_prediction_with_braker2_pipeline|[Pipeline] Gene prediction with Braker2]]
  
-[[gene_prediction_curation_with_igv| Gene prediction curation with IGV]]+[[gene_prediction_with_funannotate|[Pipeline] Gene prediction with the Funannotate]] 
 + 
 +[[automatically_fixing_gene_models|[Fix] Improving gene models with fix_genes_with_false_introns.py]] 
 + 
 +[[gene_prediction_curation_with_igv|[Manual Curation] Gene prediction curation with IGV]]
  
 [[From Nanopore to Gene Prediction]] [[From Nanopore to Gene Prediction]]
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 [[Dayana Salas - Utility scripts(taxonomy, coloring trees, phylogenetics, mixture models, domain architecture and more)]] [[Dayana Salas - Utility scripts(taxonomy, coloring trees, phylogenetics, mixture models, domain architecture and more)]]
  
 +====Protein structure prediction====
 +
 +[[Running AlphaFold at scale]]
 ====Phylogenetic analyses==== ====Phylogenetic analyses====
  
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 [[Who looks after which page]] [[Who looks after which page]]
 +
 +====== Project Documentation ======
 +
 +[[ Blastocystis orf160 ]]
 +This could possibly be an interesting project for a future undergraduate student
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