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lecture-16-handouts - Practical Bioinformatics for Life...

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10/13/2011 1 Practical Bioinformatics for Life Scientists Week 8, Lecture 16 István Albert Bioinformatics Consulting Center Penn State Disclaimer Almost everything that you learn here will be obsolete in 10 years (if we are lucky; 5 years if we are not) What will endure is the philosophy; how we approach/solve/validate tasks: using command line tools writing scripts to rerun an analysis using awk (python) to transform formats chaining one tool into another Simple questions with not so simple answers What should I do with reads that map to multiple locations? What should I do with identical (duplicated) reads? Even accurately defining these problem is difficult let alone properly answering them Strategies 1. Be aware of these problem! Know how many reads in your data are duplicated/map to multiple locations. 2. Set up your analysis so that it is easy to rerun it on a BAM file with or without certain type of reads. Evaluate the results!
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