April 9th - sellwe/Genome-Analysis GitHub Wiki

Created softlinks for the nanopore data:

[sebase@rackham1 nanopore]$ ln -s /proj/uppmax2025-3-3/Genome_Analysis/1_Zhang_2017/genomics_data/Nanopore/E745_all.fasta.gz /home/sebase/Genome-Analysis/data/raw_data/genomic/nanopore/E745_all_nanopore.fasta.gz

I also decided to check the quality of the unpaired trimmed reads as spades does support all, and if their quality is also good i will use both paired and unpaired in the spades run.

[sebase@rackham1 01_preprocessing]$ sbatch run_fastqc_trimmed_unpaired.sh

Submitted batch job 9892159 on cluster snowy [sebase@rackham1 01_preprocessing]$ pwd

/home/sebase/Genome-Analysis/code/01_preprocessing

I got an issue where i cant open the file E745_R2_unpaired_trimmed.html. It instead open E745_R1_unpaired_trimmed.fq.gz. I will try to rerun fastqc only on R2 unpaired to try to fix this.

I will need to push the spades script after performing Qual

Spades only took 25 min to run which seems suspicious