Hello, I am dealing with solexa pared-end RNA-seq data of bacteria. Now I use cufflinks tools to caculate FPKM, then I can analyze differential expression genes, but when I compare FPKM value and single-resolution coverage of a gene, I find FPKM of some genes are very high, such as, FPKM value is 4800, but each base of these genes' coverage(or number of reads) is low, such as read number of each base among a gene is about 10, so could someone help me: why the coverage of each base among a gene is so low when FPKM is very high? How to explain this? Does it need to do FPKM normalization? Thank you!
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