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Exercises

Info

We put some exercises here for you, if you want to get some more hands-on.

Working with modules

View in IGV

  • Load the genome, the bam file, and the annotated vcf that we got from the demo into IGV for viewing

    Answer

    For this small example we use igv-core. Good is also to be on a compute node.

    $ ml bioinfo-tools IGV
$ igv-core --genome genome.fa
    Then open ERR1252289.subset.bam ERR1252289.subset.snpEff.vcf.gz from the GUI.

Transferring files

Copy files between to Sens projects

  • Use the Transit server to copy a file (e.g. the interactive session script) from the Bianca workshop project to another project, if you belong to one.

    Answer
    1. Connect to transit
    2. Mount the projects with mount_wharf
    3. Move/copy the file(s) from sens2023598 to your other project.
    4. Log in to the other Sens project on Bianca and move the file from the wharf to a good place

Using the compute nodes

Submit a Slurm job
  • Make a batch job to run the demo "Hands on: Processing a BAM file to a VCF using GATK, and annotating the variants with snpEff". Ask for 2 cores for 1h.
Answer
  • edit a file using you preferred editor, named my_bio_worksflow.sh, for example, with the content
#!/bin/bash
#SBATCH -A sens2023598
#SBATCH -J workflow
#SBATCH -t 01:00:00
#SBATCH -p core
#SBATCH -n 2


cd /proj/sens2023598/workshop/slurm/

module load bioinfo-tools

# load samtools
module load samtools/1.17

# copy and example BAM file****
cp -a /proj/sens2023598/workshop/data/ERR1252289.subset.bam .

# index the BAM file
samtools index ERR1252289.subset.bam

# load the GATK module
module load GATK/4.3.0.0

# make symbolic links to the hg38 genomes
ln -s /sw/data/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.* .

# create a VCF containing inferred variants
gatk HaplotypeCaller --reference genome.fa --input ERR1252289.subset.bam --intervals chr1:100300000-100800000 --output ERR1252289.subset.vcf

# use snpEFF to annotate variants
module load snpEff/5.1
java -jar $SNPEFF_ROOT/snpEff.jar eff hg38 ERR1252289.subset.vcf > ERR1252289.subset.snpEff.vcf

# compress the annotated VCF and index it
bgzip ERR1252289.subset.snpEff.vcf
tabix -p vcf ERR1252289.subset.snpEff.vcf.gz

  • make the job script executable 

    $ chmod a+x my_bio_workflow.sh

  • submit the job 

    $ sbatch my_bio_workflow.sh

Doing installations

Rpackage installation

Install dowser
Answer

Dowser exercise

Conda installation

Install with Conda directly on Bianca
  • Install python=3.7 and numpy=1.15 with Conda directly on Bianca.
Answer

https://uppmax.github.io/bianca_workshop/conda/#exercises

Pip installation with virtual environment

Install with pip
  • Make a virtual environment (confer this tutorial) with python/3.8.7 on Rackham and install numpy==1.18.1 and matplotlib==3.1.3. Use sftp to get it to Bianca.
Answer

https://uppmax.github.io/bianca_workshop/pip/#isolatedvirtual-environments

Julia installation

Install a Julia package
  • Install Gumbo in the julia packager tutorial. Use sftp to get it to Bianca.
Answer

https://uppmax.github.io/bianca_workshop/julia/#install-yourself

Singularity/Apptainer

Install gatk on bianca with Apptainer
  • Use the docker image for gatk/4.3.0.0 and install on Rackham and transfer to Bianca.
Answer

https://uppmax.github.io/bianca_workshop/containers/#example-i-want-gatk-on-bianca