Gene Expression Annotation
Gene coverage
Gene expression levels
Gene coverage is the percentage of a gene been covered by reads.
This value equals to ratio of the number of bases in a gene covered by unique mapping reads to number of total bases in that gene
I:\00_PROJECTS\[Tv_Solexa_RNAseq]\image\rpkm.jpg
The calculation of Unigene expression uses RPKM method (Reads Per kb per Million reads)
The RPKM method is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples
C  = number of reads that uniquely aligned to gene A,
N = total number of reads that uniquely aligned to all genes,
L  = number of bases on gene A.