————————Lecture Slides——————–

ChIP-seq Methods & Analysis_pt1 ChIP-seq Methods & Analysis course Slides for day 1, Monday 2/11/2013: Introduction, ChIP method, library preparation, ChIP-seq technology, accessing ChIP-seq data on the UCSC genome browser.

ChIP-seq Methods and Analysis pt2 Slides for day 2, Tues 2/12/2013: QC on sequence data, mapping reads to the genome, identifying peaks w/ MACS.

ChIP-seq Methods and Analysis pt3 Slides for day 3, Weds 2/13/2013: Finishing up MACS analysis, analysis of peaks relative to genomic features.

ChIP-seq Methods and Analysis pt4 Slides for day 4, Thurs 2/14/2013: Analysis of enriched TF binding sites in peaks.

ChIP-seq-Methods-and-Analysis-pt5 Slides for day 5, Fri 2/15/2013: Variants & advanced techniques related to ChIP-seq.


Key R commands_10_14_2010.doc A primer on just the basic R commands you’ll need to know to run existing bioinformatics programs in R (and how to download & use these programs).

PERL_language_notes.doc Brief notes on writing programs in Perl – for beginning introductions see links under the RNA-seq course.

ChIPseq_analysis_methods_2013_02_11 This file has more detailed guidelines on how to troubleshoot MACS, etc. Some things (such as the best way to normalize & trim .bdg files) are functional, but a bit out of date.

————————Sample files——————–

Liver_ERa_Peaks_on_Chrom_19 This is a link to the MACS sample ChIP-seq results

ERa_ChIPseq_mouse_aorta_E2_Chr1.bdg This is an example bedgraph file to try downloading.