Tutorials¶
Tutorials are divided into two sections:
The Cookbook contains step-by-step instructions for performing common tasks, with detailed explanations of each step
In-depth includes longer discussions of issues that arise in high-throughput sequencing and genomics, and includes code examples when appropriate.
We suggest downloading the Demo dataset and following along.
Cookbook¶
Tutorial |
Contents |
Set up a genome for downstream analysis, using |
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Simplified workflow of how to align sequencing data |
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Retrieve a vector of high-throughput sequencing counts at each position in a transcript |
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Fetch the sequences of regions of interest (e.g. transcripts) from a genome |
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Compute gene expression measurements and translation efficicency using RNA-seq & ribosome profiling, and prepare data for differential expression analysis |
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Exclude specific regions – for example, repetitive genome sequence that gives rise to multimapping reads – from analysis. Discussion of mask files. |
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Make a BED, BigBed, GTF2, or GFF3 file containing custom features. |
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Perform metagene analysis, using ribosome profiling data at the start codon as an example. Then, develop metagene analysis around a custom landmark for use with other data types |
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Determine a P-site offset from ribosome profiling data |
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Estimate read phasing (triplet periodicity) of ribosome profiling data |
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Demos of plotting tools in |
In-depth¶
Tutorial |
Contents |
Introduction & discussion to the types of data used in genomics, and the advantages and disadvantages of their various file formats |
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Primer on the various coordinate systems used in genomics |
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Issues arising when and strategies for handling multimapping reads |
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In-depth discussion of mapping rules, with code examples of how to write your own mapping rule for your own sequencing data type |