Tutorials

Standalone tutorials, both for working through & reference purposes.

General topic: how to do basic scientific data analysis on UNIX.

Contents:

• UNIX, ssh, and scp
• Renting a computer from Amazon
• Running BLASTs on UNIX
• UNIX, BLAST, and long-running jobs
• Working with CSV files and Python
• Plotting with matplotlib
• Scripts, Reciprocal Best-Hits BLAST, and some more Python
• Mapping with bowtie
• Visualizing mappings with Samtools
• Other mappers
• Short Read Assembly
• Visualizing NGS data on UCSC genome browser
• Simple mRNAseq: mapping reads to gene sets and doing quantile normalization
• Gene differential expression using DEGseq
• Analyzing bacterial resequencing data with breseq
• Storing data persistently with Amazon
• Writing Python scripts incrementally
• Aligning ChIP-seq reads and detecting enriched peaks
• Using MEME to identify TF binding motif from ChIP-seq data
• Slightly more advanced scripting with Python
• Using the Nano editor
• Using ‘top’ to monitor running jobs
• Setting a password rather than using your key

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