For Reproducibility purposes, the steps completed have been provided in a list below. The files in this repository arranged to reflect this and contain further instruction within each folder. Details about analysis and steps can be found on the wiki along with a more detailed project plan while further instruction on running code can be found in the README.md files contained within each folder.
To determine relevant genes found in E. faecium E745 that play a role in the vancomycin-resistant strain's growth in human serum by looking at differential expression analysis between rich medium and heat-inactivated serum conditions as based off a study by Zhang (Zhang, 2017). Upon completetion, further investigation was done to investigate phage integration. Future studies might include comparison of resistance genes to prophage integration
FASTQ and FASTA files files of DNA, RNA, and Transposons
- Genome assembly of Pac-Bio DNA reads using Canu
- Vizualization of Illumina DNA sequences with FastQC
- Trimming of Illumina reads using Trimmomatic
- Mapping Illumina reads to Pac-Bio Assembly:
4.1 Using BWA-MEM to map
4.2 Converting SAM files to BAM using SAMtools
4.3 Creating a combined genome assembly from mapping using Pilon
4.4 QUAST - Annotation of the combined assembly:
5.1 Using Prokka for structural and functional annotation
5.2 Using eggNog-Mapper for functional annotation
5.3 Artemis ART and ACT used for Visualization and Synteny - RNA Mapping:
6.1 For serum RNA using BWA-MEM and converted to to BAM using SAMtools 6.2 For BHI RNA using BWA-MEM and converted to to BAM using SAMtools - Counting RNA reads:
7.1 Converting .gbk to .gtf with gbk2gtf.py
7.2 Counting serum RNA reads using HTseq-count
7.3 Counting BHI RNA reads using HTseq-count - Differential expression using DEseq2
- Interpretation and Other Analysis**
**See Results and Discussion page for the interpretation of DEseq2 and other analysis results.