Home - SIWLab/Lab_Info GitHub Wiki

This wiki serves as the Wright Lab's introduction and reference for wet and dry lab protocols and tips. View the links below and check the sidebar for useful info.

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Lab guide

** read the lab guide here https://github.com/SIWLab/Lab_Info/wiki/Lab-guide

Computing 🖥️

• Read the Rules and Regulations page
• Using the servers: grandiflora, capsicum, ohta, and gustave info
• Git resources: How to use git & GitHub
• Code styleguides: Make sure your code is easy to read and understand
• Using vim and other text editors

outside resources

• File formats in bioinfo
• Basic linux commands
• linux top command output explained

Bioinformatic tools and pipelines 🔧

• Aligning RNA seq data with STAR
• Variant calling with freebayes
• Samtools, Picard, and GATK variant calling pipeline
• Aging LTR insertions

older tools - please consult more recent documentation before using

• Running barraCUDA- use bwa-mem2 instead
• Running hapCUT to obtain putative haplotype blocks

Lab Protocols 🧪

• Wetlab protocols: safety first! Make sure your WHMIS/EHS training is up-to-date
• Qiagen kit Rumex DNA extraction
• Sorbitol-CTAB Rumex DNA extraction

Facilities Information and Contacts ☎️

• ESC
• Growth facilities
• Lab
• EEB department
• IT

Lab calendar 📆

Wright lab calendar on outlook, ask Stephen to be included.