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] | |||
== See also == | == See also == | ||
Revision as of 10:01, 6 March 2015
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] | Variant annotation tutorial]