Summary and Schedule

Setup

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Two scenarios:

• JAX: No setup required. Just need sumner access & terminal program.
• Outside:
  • install nextflow (beyond scope),
  • configure nextflow profile for local computing environment,
  • install Singularity (will Docker work?),
  • get Singularity containers from ???,
  • get reference files Zenodo,

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Genotyping by RNA Sequencing	What is Genotyping by RNA Sequencing (GBRS)? What analyses does GBRS provide? What are the steps in a GBRS analysis?
Duration: 00h 12m	2. Installing GBRS	What supporting software is needed to install GBRS? How do I configure my installation for my computing cluster? Where do I obtain the GBRS reference files?
Duration: 00h 47m	3. Running GBRS	How do I run GBRS on my FASTQ files at JAX? How do I run GBRS on my FASTQ files at another institution?
Duration: 02h 47m	4. Preparing GBRS Pseudo-References	Why do we need to align to a non-reference genome? What is a pseudo-reference genome? How do we create a pseudo-reference genome?
Duration: 04h 02m	5. Prepare EMASE Reference Files	What does the Prepare EMASE process do? What input files are required to prepare the EMASE reference? What output files are created by the Prepare EMASE process?
Duration: 04h 14m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Data Sets

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If you are working outside of The Jackson Laboratory, you will need to download the reference FASTA and GTF file from: Zenodo.

Specifically, you should download:

• Ensembl 105 GTF
• GRCm39 FASTA
• GRCm39 FASTA Index

You should also download the mouse SNP and Indel files from the Mouse Genomes Proejct.

• SNP VCF
• SNP VCF Index
• Indel VCF
• Indel VCF Index

Software Setup

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Details

You will be using a terminal window to connect to your computing cluster via secure shell (ssh). See the links below for different operating systems to see which program to use.

Windows

We recommend MobaXterm for connecting to external systems.

MacOS

Mac/OS has a Terminal.app that can connect to external systems.

Linux

Linux systems have a terminal and should have ssh installed to connect to external systems.