Welcome to Nicholas McGranahan lab!

We complied a short guide for you to help you with the overwhelming amount of information you might face upon your arrival. Please see below for the links to the pages which might be interesting for you. Links to the pages are also available at the right hand side of the screen, but due to their quite large amount the list is truncated.

Lab meetings & presentations:

Book and use the UCL CI 1st floor meeting room

Getting access:

• 002 Getting UCL email address

• 003 Getting Crick email address

• 004 Getting access to UCL cluster

• 005: Getting access to Genomics England (GEL)

Coding practices:

• 006 Introduction to statistics & coding: helpful resources

• 007 Coding practices for clear, clean and understandable code

• 008 Standard project structure

• 009 GitHub tutorial

• 010: UCL cluster: a tutorial for beginners

Nextflow:

• 011 Nextflow basics & project structure

• 012: Nextflow execution on UCL cluster

• 013: Using the TCGA data on the UCL cluster

Singularity:

• 014: Singularity, part 1: installation of Singularity on Mac OS

• 015: Singularity, part 2: anatomy of Singularity's recipe

• 016: Singularity, part 3: singularity on cloud

Genomics England (GEL):

• [Working on GEL basics]https://github.com/McGranahanLab/Guidebook/wiki/GEL-basics

GWAS:

• 017: GWAS with PLINK

EGA

• 018: Upload files to EGA and get EGA ID

Alignment with GPUs and Parabricks on UCL cluster

• 019: Alignment with GPUs and Parabricks on UCL cluster