lecture-21 - Practical Bioinformatics for Life Scientists...

Info iconThis preview shows pages 1–14. Sign up to view the full content.

View Full Document Right Arrow Icon
Practical Bioinformatics for Life Scientists Week 11, Lecture 21 István Albert Bioinformatics Consulting Center Penn State
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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
Background image of page 2
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
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
With bedgraph coverage
Background image of page 4
CEAS: Cis-regulatory Element Annotation System Creates a PDF report on the data See pdf report on the course webpage.
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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
Background image of page 6
Requires MySQL installation The genome builder requires the MySQL database installation this can be tedious and we’ll skip this step – there will be an in class demonstration on how the genome builder works
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 8
Background image of page 9

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 10
Background image of page 11

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 12
Background image of page 13

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 14
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

Page1 / 14

lecture-21 - Practical Bioinformatics for Life Scientists...

This preview shows document pages 1 - 14. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online