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Applied-Bioinformatics

Student course material for the Applied Bioinformatics course at Scripps Research for fall 2018.

Prerequisites

The only requirement is that you have access to a latop running Windows 10 or macOS, and that you complete:

Course materials

Module 1: Bash, Juypter and git

1.1 Course intro:

1.2 Bash basics

1.3 Jupyter basics

1.4 File manipulation

1.5 Redirection and pipes

1.6 awk

1.7 git

1.8 looping

Yolanda's handouts

Module 2: R

2.1 R objects

2.2 R data operations

2.3 and 2.4 Flowchart & review

2.5 Exploratory Data Analysis and Plotting

Module 3: RNA-seq

3.0 RNA-seq overview

3.1 Raw data

3.2 SAM files and gene counting

3.3 Counts-based expression analysis

3.4 Preparing data for DESeq2

3.5 Gene expression analysis with DESeq2

3.6 Differential expression analysis

3.7 Enrichment analysis

Module 4: ChIP-seq

4.1 ChIP-seq basics

4.2 ChIP-seq filter and alignment

4.3 Customized filter and MACS2 peak calling

# Ubuntu terminal Option #1
scp [email protected]:/gpfs/home/hdiao/bam/target_file    Your_directory

# Ubuntu terminal Option #2
# click the links and download to your `Downloads` directory, then copy using this command template below:
cp /mnt/c/Users/<username>/Downloads/SRR3001750_srt_dupr.chr10.bam .

4.4 ChIP-seq data visualization & general tips for fixing bugs

4.5 ChIPQC and Transcription Factor Consensus Motif Enrichment by Homer