Zero FPKM at some Cufflinks output file

[fuad193]

Hi

Some transcripts at the final output of cufflinks have zero FPKM and coverage. I am using annotation from ensembl (annotation_ensembl.gtf). This is my command line:

cufflinks -p 8 -G annotation_ensembl.gtf -b genome.fa aln.sam.sorted

aln.sam is produced via bowtie and the aligned reads were 75%. I don't think the problem is in the sam file.

[kopi-o]

I don't think there is necessary any problem. Earlier versions of Cufflinks used to output only transcripts with non-zero FPKM, but later versions output values for all transcripts that you have provided. So whether you are genuinely having a problem would depend on which version you are using.