Aidan Coyle's repository for FISH 546, Winter 2021 Contact info: [email protected] Roberts Lab, UW-SAFS
This repository contains a series of smaller projects completed as part of Steven Roberts' Bioinformatics class at UW-SAFS, Winter 2021. Projects are all contained in subdirectories within projects/
2021-01-18_Intro_to_Blastx:
Compared a set of nucleotide sequences to Swiss-Prot sequences using BLAST. All relevant code in Jupyter Notebook within folder.
Nucleotide sequences downloaded from here at 20:00 PST on 2021-01-18. Command is documented within Jupyter notebook.
Swiss-Prot sequences downloaded from here at 19:00 PST on 2021-01-18. Command and MD5 checksum are documented in Jupyter notebook.
2021-01-25_Data_Exploration
Practiced exploring .fastq files running FastQC on a .fastq library. Nucleotide sequence downloaded from here on 2021-01-25
hematodinium_analysis
This is an offshoot of my research for the Roberts lab so far. The central aim is to analyze differential expression in Hematodinium. Samples are taken from Hematodinium-infected Chionoecetes bairdi. To view the most up-to-date information, please go to my main repo. If you are looking for more detailed information as part of FISH 546, in-depth info describing process/workflow/plan for the future is found in the README file within the projects/hematodinium_analysis directory of this repository.
My presentation can be found here
My methods can be found here