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