Daily log - saltpinna/Genome_analysis_project GitHub Wiki

22-03-23

GitHub repository and Wiki created

22-03-24

Introductory Lab seminar

22-03-28

Started working on the project plan

22-03-29

Finished project plan + handed in on Studium. Also added this GitHub repository to the form on the course page.

22-03-30

Today I started the project. I created a script for the genome assembly in Canu and submitted it as a batch job to snowy (see script in code section of this repoistory on GitHub). I also performed the FastQC quality check before trimming of the Illumina reads, this batch script is also available in the repository. I started creating a script for trimming the Illumina reads in Trimmomatic, but could not get it to work. I got a lot of different errors and still haven't gotten it to work. Anna said she would look at the code and help me try to find what can be the problem. After looking at the result from the FastQC before trimming (on raw Illumina reads), I decided trailing above a threshold of 20 would be fitting since a lot of the last positions in the reverse sequence has low quality.

22-04-05

Today, I performed a quality evaluation of the Genome assembly using Quast. I also did a funcitonal annotation using Prokka.

22-05-03

Started working on the scripts for BWA alignment and htseq read counting. To save disk space, the BWA alignment and RNA read counting with htseq were piped together in one script (one for BW and one for serum) to avoid creating large output files on the small project disk space. Also started working on the Spades script for Genome assembly using Illumina + nanopore reads in Spades. Did not get this to work yet, but working on it. The resulting slurm-file was completely empty so I do not know what went wrong.

22-05-06

Continued working with the scripts for BWA alignment as well as Spades. Got Spades to work and added the script + results to Github.

22-05-07

Finished scripts for BWA alignment and uploaded them + results to Github.