Table of Contents

Fall '24 BMMB 852 Applied Bioinformatics Class Coding Projects and Scripts.

• Wk1 contains week 1 assignment in .txt format.

• Wk2 contains week 2 assignment in .txt and .md files. The assigment was to demonstrate data analysis using UNIX command lines and produce results. The GFF file used was from https://ftp.ensembl.org/pub/current_gff3/coturnix_japonica/

• Wk3 directory has Wk3_Assignment_StephanieWon.md, images, and GFF files using IGV interface and terminal. Note CDS.gff (150 MB) is compressed into zip file due to GitHub file size limit.

• Wk4 contains scripts for the assignment. wk4_part2.sh is script for the Sequence Ontology section. The sequence_ontology directory contains the TXT file of the pseudogene feature report.

• Wk5 contains scripts and markdown report for the assignment. fastq_report.sh is the script for answering Question 1 and fastq_simulation.sh is the script for answering Question 2 and Question 3 of the assignment. fastq_simulaton.sh is simulating reads using various sequencing models.

• Wk6 contains script and markdown report for FASTQ quality control assignment. The directory contains image files in relation to the assignment.

• Wk7 contains makefile and markdown report using previous assignment

• Wk8 contains makefile that generates BAM alignment file and markdown report of the alignment result.

• Wk9 contains the markdown and flagstat reports (.txt files) as well as makefile.

• Wk_10 contains the markdown report and makefile for variant calling assignment.

• Wk_11 contains the markdown report and makefile for variant effect predition.

• Wk_12 contians the markdown report and makefile for automate a VCF calling pipeline.

• Wk_13 contains the markdown report and makefile for generating RNA-seq count.

• Wk_14 contains the markdown report and makefile for differential expression result and analysis.