Bioinformatics tips tricks workflows: Difference between revisions
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* [[calculate_corrected_theta_from_resequencing_data | Calculate nucleotide diversity (theta) corrected for sequencing depth]] | * [[calculate_corrected_theta_from_resequencing_data | Calculate nucleotide diversity (theta) corrected for sequencing depth]] | ||
* [[RNA-seq analysis | RNA-seq analysis with Tophat]] | * [[RNA-seq analysis | RNA-seq analysis with Tophat]] | ||
* [[Variant_annotation_tutorial | * [[Variant_annotation_tutorial | Variant annotation tutorial]] | ||
* [[issues_asreml | Issues with ASReml]] | |||
* [[Checkpointing | Checkpointing]] | |||
* [[ | * [[Assembly & Annotation | Assembly and Annotation guidelines (denovo)]] | ||
* [[DE expression | DE expression analysis with tophat2 / cuffdiff]] | |||
* [[JBrowse | JBrowse]] | |||
* [[Running Snakemake pipelines | Running Snakemake pipelines]] | |||
* [[Mapping and variant calling pipeline | Mapping and variant calling pipeline]] | |||
* [[Population structural variant calling pipeline | Population structural variant calling pipeline]] | |||
* [[Population mapping pipeline | Population mapping pipeline]] | |||
* [[Nanopore assembly and variant calling| Nanopore assembly and variant calling pipeline]] | |||
* [[Population variant calling pipeline | Population variant calling pipeline]] | |||
* [[Single Cell preprocessing pipeline| Single Cell preprocessing pipeline]] | |||
* [[Whole genome alignment pipeline | Whole genome alignment pipeline]] | |||
== External links == | == External links == | ||
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages] | * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages] | ||
Latest revision as of 14:41, 18 July 2022
This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts).
A list of tutorials, workflows, and recipes
- Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly
- A Perl script to convert fastq to fasta file format
- Mapping Pair-end reads with Stampy
- Create slices from a collection of BAM files
- Setting up and using a virtual environment for Python3
- ssh without password
- Create a shortcut for the ssh log-in command
- Installing R packages locally
- Command-line tricks for manipulating fastq files
- Assemble mitochondrial genomes from whole-genome short-read data
- 1000 Bulls mapping pipeline at ABGC
- Animal Breeding and Genomics Sequence Archives (ABGSA)
- Pig mapping pipeline at ABGC
- Extract a set of pig SNPs not called in a control sample (soybean)
- Calculate nucleotide diversity (theta) corrected for sequencing depth
- RNA-seq analysis with Tophat
- Variant annotation tutorial
- Issues with ASReml
- Checkpointing
- Assembly and Annotation guidelines (denovo)
- DE expression analysis with tophat2 / cuffdiff
- JBrowse
- Running Snakemake pipelines
- Mapping and variant calling pipeline
- Population structural variant calling pipeline
- Population mapping pipeline
- Nanopore assembly and variant calling pipeline
- Population variant calling pipeline
- Single Cell preprocessing pipeline
- Whole genome alignment pipeline