Bioinformatics tips tricks workflows

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
• Mapping and variant calling pipeline

External links

• Help with editing Wiki pages