Today I tried to use FPKM to obtain the expression characteristic of my interested gene in specified tissue based on RNA-seq.
My operation is follows:
1. Converted sra (download from NCBI) file to fastq file and then converted it to fasta file(RNA-seq data);
2. Blast was used to find fragments which have zero E-value to interested gene
3. Extracted information of these fragments trough fastq file and then converted it as fastq format
4. Bowtie2 and cufflinks were used to calculate the FPKM values associated with reference genome
In the out file of cufflinks, such as gene.fpkm_tracking and others, the FPKM values were not only one. So I don't know how to use these FPKM values indicate interested gene expression, average value or total value ?