Logs.md

Logs

Dates

4/4

• Draft preliminary project plan
• Understand the data
• Create soft links to data in the project folders
• Genome assembly by Canu
  • input: ~/genome_analysis/data/DNA_raw_data/
  • output: ~/genome_analysis/analyses/01_genome_assembly/01-lfts-pacbio/

4/5

• Organize working directory
• Assembly quality check by Quast
  • input: ~/genome_analysis/analyses/01_genome_assembly/01-lfts-pacbio/lfts.contigs.fasta
  • reference: ~/genome_analysis/data/reference/OBMB01.fasta
  • output: ~/genome_analysis/analyses/02_assembly_quality_assessment/01-quast/

4/11

• Genome annotation by Prokka
  • input: ~/genome_analysis/analyses/01_genome_assembly/01-lfts-pacbio/lfts.contigs.fasta
  • output: ~/genome_analysis/analyses/03_genome_annotation/01-prokka/
• RNA-seq reads quality check before trimming by FastQC
  • input: ~/genome_analysis/data/RNA_raw_data/
  • output: ~/genome_analysis/analyses/04_rna_preprocessing/01-fastqc/
• RNA-seq trimming by Trimmomatic
  • input: ~/genome_analysis/data/RNA_raw_data/
  • output: ~/genome_analysis/analyses/04_rna_preprocessing/02-trimmomatic/
  • the trimlog file and trimming results files are too large, so remove them and use provided data instead

4/12

• Assembly quality check by MUMmer
  • input: ~/genome_analysis/analyses/01_genome_assembly/01-lfts-pacbio/lfts.contigs.fasta
  • reference: ~/genome_analysis/data/reference/OBMB01.fasta
  • output: ~/genome_analysis/analyses/02_assembly_quality_assessment/02-mummer/
• RNA-seq reads quality check after trimming by FastQC
  • input: ~/genome_analysis/data/RNA_trimmed_reads/
  • output: ~/genome_analysis/analyses/04_rna_preprocessing/03-fastqc/

4/24

• RNA mapping by BWA
  • input: ~/genome_analysis/data/RNA_trimmed_reads/
    ~/genome_analysis/analyses/01_genome_assembly/01-lfts-pacbio/lfts.contigs.fasta
  • output: ~/genome_analysis/analyses/05_rna_mapping/01_bwa/

4/25

• Functional annotation by eggNOGmapper (online)
  • input: ~/genome_analysis/analyses/03_genome_annotation/01-prokka/lfts.faa
  • output: ~/genome_analysis/analyses/03_genome_annotation/02-emapper/lfts.faa.emapper.annotations
    http://eggnogdb.embl.de/#/app/emapper?jobname=MM_enfDAg
• Synteny comparison with closely related genome by blast
  ~/genome_analysis/analyses/01_genome_assembly/01-lfts-pacbio/lfts.contigs.fasta
  Leptospirillum ferriphilum ML-04
  Leptospirillum ferriphilum YSK

5/2

• Discard half of bam files because of duplicates, around 3GB of one file
• Read counting by HTSeq
  • input: ~/genome_analysis/analyses/05_rna_mapping/01_bwa/
    ~/genome_analysis/analyses/05_rna_mapping/02_htseq/lfts.gff
  • output: ~/genome_analysis/analyses/05_rna_mapping/02_htseq/

5/7-5/24

• Differential analysis by DESeq2
• Redo some steps with different options to compare results
• Extra analysis, compare with paper