lecture-20 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 10, Lecture 20 István Albert Bioinformatics Consulting Center Penn State
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bioawk chipfrag.awk Pull from the bioawk repository Estimate chip-seq DNA fragment size Simple: Count the number of times reads on one strand overlap with reads on the other strands for different shifts on the forward strand This problem, once solved, will be simple. ― Thomas A. Edison
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Today’s starting point
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Looping in bash- run the fragment estimator for multiple shift values
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Plotting shifts 0 to 200
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ChipSeq Challenge Comparing multiple peak callers for accuracy Issues with validation There is a final report see course webpage for the link
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Summary of the ChipSeq challenge Two categories 1. Discrimination between true positives and false positives MACS , USeq , Partek , SWEMBL , and BPC performed well 2. Accurate confidence estimation in a given list of candidate binding peaks Cisgenome , Useq performed well
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lecture-20 - Practical Bioinformatics for Life Scientists...

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