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.
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.
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