Inclass Activities

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Bioinformatics part I

1. Multiple Sequence Alignments
2. Steps of building a tree
3. Steps of building a tree (Part II)

High-throughput data analysis

FastQC analysis using Cyverse Discovery Environment (DE)
Relaunching a stalled analysis in Cyverse Discovery Environment
Adapter and quality trimming using trim-galore
Mapping short reads
Counting mapped reads
Differential gene expression analysis

Protein analysis

Secondary Structure Prediction
Tertiary Structure Prediction

qPCR data analysis

The Delta-Delta Ct Method

Galaxy for HTS analysis

Getting data into Galaxy
FastQC analysis using Galaxy
Adapter and quality trimming using Cutadapt
Adapter and quality trimming using trim-galore
Use Splice aware aligner, Tophat2 to align short reads
Use Htseq to counts reads mapped to features
Use Kellisto to map reads to cDNA and count
Setup instructions (This is from Data Carpentry (http://www.datacarpentry.org/R-genomics/))
Using DEseq and EdgeR to find differentially expressed genes
DEseq analysis
Combine DESeq and EdgR to make Venn diagram
GOseq analysis
Run RNAseq analysis as a workflow

Inclass Activities

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Run RNAseq analysis as a workflow
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Run RNAseq analysis as a workflow¶

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