We are just starting to migrate our tutorials to a gitbook and will be creating a comprehensive bioinformatics workbook with examples that can be run on any machine.
Please revisit in the near future and check out our progress.
In order to apply bioinformatics to a question in biology, an individual must understand the assumptions and limitations of the sample, the sequencing technology, and the software.
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Sample - The tissue, characteristics of the genome, contamination, and biological question of interest affect how to interpret results.
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Sequencing Technology - read length, paired/unpaired reads, types of errors, contamination, and adapters need to be considered when analyzing the data
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Software - The author of the open source software likely had a specific biological question in mind with assumptions on the sequencing technology and sample that the software can handle. Knowing these assumptions and limitations will determine if you can use it for your question