Hello all,
I have been using the tophat/cufflinks approach to analyze some fetal and neonate liver mRNA sequence and I have run across the issue of 'HIDATA' in the FPKM status column. The issue I'm having is that most of the genes of interest (albumin, alphafetoprotein, apolipoproteins, etc) all have the HIDATA status in cuffdiff output and thus have FPKM values of zero. My questions are as follows:
1) Why does cufflinks have difficulty testing those genes with a high number aligned fragments?
2) Has anyone encountered this phenomenon, and, if so, how did you address the issue?
Thanks
I have been using the tophat/cufflinks approach to analyze some fetal and neonate liver mRNA sequence and I have run across the issue of 'HIDATA' in the FPKM status column. The issue I'm having is that most of the genes of interest (albumin, alphafetoprotein, apolipoproteins, etc) all have the HIDATA status in cuffdiff output and thus have FPKM values of zero. My questions are as follows:
1) Why does cufflinks have difficulty testing those genes with a high number aligned fragments?
2) Has anyone encountered this phenomenon, and, if so, how did you address the issue?
Thanks
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