Talk given at ECCB 2014 workshop: http://www.eccb14.org/program/workshops/rna-seq, and at University of Zurich, on tools we've built to do differential expression analysis without relying on existing gene/exon/isoform annotation.
0 2 4 6 8 log2(count+1) chr22: 17684448−17684670 normal tumor −1 0 1 2 3 4 5 t statistic xaxinds exons states 17684041 17684451 17684551 17684651 17684754 genomic position match to annotation if desired:
CECR1, “may play a role in regulating cell proliferation”
easy exploration and DE analysis
annotation functions
24615000 24620000 24625000 24630000 24635000 24640000 genomic position Assembled and Annotated Transcripts annotated assembled get corresponding gene names, match assembled and annotated transcripts, plot assembly alongside annotation
freely available!
Bioconductor (devel):
source(“http://bioconductor.org/biocLite.R”) biocLite(“ballgown”) GitHub:
https://github.com/alyssafrazee/ballgown
Cufflinks users will also need Tablemaker:
https://github.com/alyssafrazee/tablemaker
differential expression model
for each transcript, compare the fits of the following models using an F-test. Null hypothesis is that the fits of model (a) and model (b) are equally good; alternative is that (a) fits better.
(a)
(b)
BRIEF ARTICLE THE AUTHOR expressioni = ↵ + 0groupi + P X p=1 pconfounderip + noiseip expressioni = ↵⇤ + P X p=1 ⇤ pconfounderip + noise ⇤ ip expressioni = ↵ + K X k=1 ksplinek(timei) + P X p=1 pconfounderip + noiseip P