Hello,
I work with solexa paired-end RNA-seq data of bacteria. I analyze differential gene expression by FPKM from cufflinks,and analyze FPKM using DEGseq to get differential expression genes. I have different strains of bacteria, and their genomes are pretty similar, but not identical. that means, I get FPKM from cufflinks for different strains using different reference and different annotation files(that is different gtf files), then can I directly compare FPKM, if not, how can I normalize FPKM to analyze different strain?
I am looking forward to your reply. Thank you!
I work with solexa paired-end RNA-seq data of bacteria. I analyze differential gene expression by FPKM from cufflinks,and analyze FPKM using DEGseq to get differential expression genes. I have different strains of bacteria, and their genomes are pretty similar, but not identical. that means, I get FPKM from cufflinks for different strains using different reference and different annotation files(that is different gtf files), then can I directly compare FPKM, if not, how can I normalize FPKM to analyze different strain?
I am looking forward to your reply. Thank you!
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