lecture-18-handouts - 10/20/2011 Practical Bioinformatics...

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10/20/2011 1 Practical Bioinformatics for Life Scientists Week 9, Lecture 18 István Albert Bioinformatics Consulting Center Penn State Aligner ROC quality plots compare Heng Li’s ROC plot versus the data shown in Prof Salzberg’s presentation Who is right? – (around the end of the semester we’ll run these tests ourselves) Twitter hashtag: #deepseq Fresh off the internets: split fasta file by Pierre Lindenbaum on BioStar Creates a new file for every N number of FASTA sequences Note: you can also use pyfasta split n 6 long.fasta
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10/20/2011 2 Back to Chip-Seq Identify bound locations then 1. tabulate the observations protein X binds at locations Y 2. compare between samples to detect different level of occupancy 3. extract sequences for binding locations and find motifs 4. study common attributes of genomic features nearby bound locations Beware of Black Boxes The more sophisticated a method the less likely is that we understand its limitations and applicability ! In general always
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lecture-18-handouts - 10/20/2011 Practical Bioinformatics...

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