May 2015 Feng Lab meeting ChIP-Seq Hands-on¶
Hands-on ChIP-Seq Analysis Workshop for Feng Lab Group meeting by Wayne Decatur
3:30am-5:20pm, May 14th, 2015.
This is the 3rd session in series; see first and second session info here
Links¶
Contents¶
- Getting started
- Logging into your computer instance “in the cloud” (Windows version)
- Logging into your computer instance “in the cloud” (NON-Windows version; for Mac and Linux)
- Overview
- Initial steps condensed for today
- STEP# 1: Get proper resources for working on genome of interest
- STEP #2: Acquire experimental data
- Extract the Gal4 reads based on barcode
- Mapping reads
- Improving the mapping of the reads
- Preliminary view of mappings
- Peak Predictions with MACS
- Peaks relative to known genomic features with CEAS
- Optional: Look at reads and/or peaks in IGB or IGV or SeqMonk OR UCSC genome browser
- Comparison to published data
- Motif discovery with MEME
- Sources
- Going forward
- Appendix: Help getting files on and off Amazon AWS EC2 instances
- Appendix: Making Wiggle file Covering Genome
- Appendix: Obtaining a BED of Telomere sequences
- Appendix: Technical guide to the workshop
- Appendix: Setting up a Mac for the workshop
- Appendix: Setting up an Amzon EC2 instance for the workshop