FengLabWkshopMay2015
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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
FengLabWkshopMay2015
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