Biostar Handbook  •  Contact email

Learn Bioinformatics in 100 hours

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In the Fall semester of 2017 this course will track the BMMB:852 Applied Bioinformatics course offered at Penn State. Use the web version of the book for the most up to date information. The PDFs may be updated with a delay.

Materials will appear twice a week on Monday and Wednesday in the order that they are presented in class. The lectures consist of slides, links to various chapters, links to supporting materials and homework. There are no videos/soundtracks at this time though we might add these in the future.

The course starts on Aug 21st and runs until December 9, 2017. Please consult the synopsis for details on what is covered and how to learn the materials.

Lecture
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Lecture 1: How is Bioinformatics practiced?

Course structure. How is bioinformatics practiced. Computer setup.

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Lecture 2: How do I use the command line?

Unix command line use. Find help on commands. Flag system.

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Lecture 3: How are Unix commands used for data analysis?

Examples of processing biological data from the command line.

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Lecture 4: What do the words mean?

How to make sense of terminology. Sequence and gene ontologies.

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Lecture 5: How to interpret a list of genes?

Functional enrichment, functional over-representation.

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Lecture 6: How to access published data from the command line

Reproducibility. Data repositories. Accessing data with Entrez Direct

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Lecture 7: Data formats. Genbank, FASTA and FASTQ

Accessing and manipulating sequencing data.

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Lecture 8: Quality control of high throughput sequencing data

Quality visualization. Improving data quality. Adapter removal.

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Lecture 9: Advanced quality control of FASTQ data

Sequence duplication, read merging, MultiQC, error correction.

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Lecture 10: Accessing the Short Read Archive

Downloading sequencing data from the SRA

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Lecture 11: Scripting and Automation

Automating repetitive tasks

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Lecture 12: Sequence Alignments

Local and global alignments. Scoring matrices.

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Lecture 13: Basic Local Alignment Search Tool, BLAST

Installing and using BLAST, search strategies, configuration.

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Lecture 14: BLAST Databases

More tips on using Blast. Interacting with blast databases.

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Lecture 15: Using Short Read Aligners

High troughput aligners and mappers: bwa, bowtie

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Lecture 16: Sequence Alignment Maps (SAM)

Understanding the SAM format

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Lecture 17: Working with SAM/BAM files.

SAM/BAM the workhorse of high throughput sequencing

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Lecture 18: Advanced analysis of BAM files.

Advanced SAM/BAM analysis

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Lecture 19: Sequencing Data Visualization

IGV the Integrative Genomics Viewer and other visualization tools

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Lecture 20: Visualizing Genomic Variation

## Objectives## Presentation## Materials## Homework

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Lecture 21: Calling SNPs. Genomic Variation Detection.

variation, pileups, SNPs, SNVs

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Lecture 22: The Variant Call Format

Understand the VCF format.

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Lecture 23: Variant Calling in Practice

Lecture 23

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Lecture 24: Multi sample variant calling

Multi sample variant calling

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Lecture 25: Introduction to RNA-Seq

rna-seq data analysis

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Lecture 26: Differential Expression with RNA-Seq

Lecture 26

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Course Synopsis: How does this course work?

What is the structure and purpose of this course.

Biostar Handbook  •  Contact email