Assignment of BIM3007 (Computational Genomics and Proteomcis)
The requirement of each assignment is in the same folder. Usually named as Assignment x.pdf (or .word). My own work is shown in .md or .tex file.
The first assignment (in the A1 folder) includes summaries about "Human genome project", "Evolution of Sequencing Techonology", "Exome-sequencing data analysis" and "Genome-wide association study".
The second assignment (in the A2 folder) includes hands-on experience to polish and evaluate an E. coli genome, conduct NIPT data analysis and variant calling of whole-exome sequencing data.
The third assignment (in the A3 folder) is to use PLINK to perform quality control steps and conduct genome-wide association study (GWAS) on the QCed data.
The fourth assignment (in the A4 folder) includes short answer question and coding exercise. The SAQ is about the data processing steps for RNA-seq. In the coding exercise, I wrote a python script to extract the positive ubiquitination sequences and the negative sequences from dataset, use CD-HIT to remove the highly similar sequences, and applied WebLogo to visualize the differences between positive and negative sets.