lecture-12 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 6, Lecture 12 István Albert Bioinformatics Consulting Center Penn State
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Possible homework 10 solution
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A few awk scripts to simplify our datasets
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Examples of interval related tasks Finding intervals relative to one another for each feature find the intervals from another dataset that are close/overlapping with it for each interval on one strand find the closest on the other strand An interval is not a point! - the question needs to be specified more precisely
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Overlap/intersect Two features are said to overlap or intersect if they share at least one base in common. Feature A Feature B Feature C genome
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Other important details What are the anchor points (the locations that represent the intervals) Which direction does the comparison proceed upstream, downstream? Often (always?) we need to create another transformed interval data that conforms to what we actually need midpoint starts upstream
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BedTools High performance software package that operates on
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lecture-12 - Practical Bioinformatics for Life Scientists...

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