lecture-21-handouts

lecture-21-handouts - 11/1/2011 Practical Bioinformatics...

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11/1/2011 1 Practical Bioinformatics for Life Scientists Week 11, Lecture 21 István Albert Bioinformatics Consulting Center Penn State Pull from bioawk and chipexo added new functionality to the command line genetrack new awk programs: 1. chopgff reduces intervals (opposite of slopBed) 2. profile.awk computes feature density Data preparation Peak calling new flag: -b (generate the smoothed signal that was used for peak calling as separate files for the forward/reverse strands With bedgraph coverage
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2 CEAS: Cis-regulatory Element Annotation System Creates a PDF report on the data See pdf report on the course webpage. CEAS command line Two step process: 1. download or create a feature database that contains 2. process your data against this feature database Precompiled feature datasets for: human , mouse , worm and fly We need to create our own for yeast Requires MySQL installation The genome builder requires the MySQL database installation this can be tedious and we’ll skip this step –
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lecture-21-handouts - 11/1/2011 Practical Bioinformatics...

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