Log - linnasp/GenomeAnalysis_VT2026_Lab GitHub Wiki

20260415

• Written and sent slerm for quality control with FastQC with the raw Illumina reads
• Written and sent slerm for trimming with Trimmomatic with the raw Illumina reads
• Written and sent slerm for quality control with FastQC with results from Trimmomatic

20260416

• Written slurm for BAM and SAMtools
• Written slurm for Pilon
• Written slurm for Quast
• Started to write slurm for BUSCO

20260420

• Run Flye

20260421

• Run BWA and SAMtools together
• Written slurm for BUSCO
• Written slurm for RepeatMasker
• Started to write slurm for BRAKER3
• Started running Pilon (finished)
• Written slurm for RepeatModeler
• Run Quast (finished)
• Run BUSCO (finished)
• Run RepeatModeler (finished)
• Run RepeatMasker (finished)
• Write slurm for FastQC for raw RNA seq
• Write outline for slurm for Trimmomatic for RNA seq

20260422

• Ran FastQC for RNA seq

20260423

• Run MultiQC for FastQC for RNA seq
• Finished slurm for Trimmomatic for RNA seq
• Run Trimmomatic for RNA seq
• Wrote slurm for FastQC for trimmed RNA seq
• Wrote slurm for MultiQC for FastQC for trimmed RNA seq

20260423

• Run Trimmomatic for each file one by one
• Started slurm for HISAT2 (and STAR)

20260428

• Run FastQC for trimmed RNA
• Created slurm for index and mapping with Hisat2
• Ran MultiQC after trimmed sequences
• Run Hisat2
• Create slurm for BRAKER3
• Create outline-slurm for eggNOG mapper
• Create outline-slurm for featureCounts
• Started running BRAKER3

20260430

• Re-run BRAKER3