gene detection

differential expression detection

Illumina RNA-Seq Analysis

Quote from "Illumina: RNA-Seq Data Comparison with Gene Expression Microarrays"

RNA-Seq sequencing reads were aligned to the reference genome by TopHat. Output
SAM files were converted to gene-level read counts using htseq-count, an
open-source tool available from EMBL10.  Fold-change ratios (in log space) were
constructed between samples and differential expression was quantified using a
Fisher Exact Test on the total number of mapped reads per gene symbol. As with
the microarray data, a fold-change cutoff of 2 and p-value threshold 0.05 were
used to determine differential gene expression. A threshold of *10 mapped reads*
was used to define detection at the gene level.

RNA-Seq papers

• Improving RNA-Seq expression estimates by correcting for fragment bias
• RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
• RNA-Seq gene expression estimation with read mapping uncertainty
• RNA-Seq - Wikipedia