80% of FPKM values are zero after cufflinks

Question

[haipingl]

I can map all the RNA-seq reads on the chromosome, but after cufflinks process, most of the FPKM values are zero. for example, there is gene fragments mapped on chromosome 11 using IGV software, but after cufflinks, the FPKM values for all the genes are zero. Any can help explain what's wrong with it. Many thanks.

[Sean Davis]

Did you check to make sure that your annotation matches the genome build with which you did your alignment?

[andrew.j.skelton73]

It'd help if you included code.

[haipingl]

Yes, the annotation is matching the genome, because some of the samples have good FPKM values. the following is the code i used: cufflinks -o output_file_name -p 20 -G annotation.gtf input_file.sort.bam

Thanks so much for your information.