Quantitative High-Throughput Sequencing

BIOS 691-804; Fall 2008
Instructor: Dr. Mark Reimers, VCU



Shirley Liu's MACS paper and its Supplement.
The first comparison of RNA-Seq and microarrays, and its Supplement.

HW # 3

Here is the data set.

1. The RNA data frame represents an idealized RNA-Seq experiment. Find the genes differentially expressed between lanes 1 and 2.

2. The ChIP data frame represents an idealized ChIP-Seq experiment. The locations of tags are given, but not strand. Find where the ChIP sample is enriched relative to the control. Use the reasoning behind the MACS, but don't copy it slavishly.