Why I get different FPKM values if I run a BAM file on cufflinks alone and on cuffdiff against another BAM file ? Aren't FPkM values consistant irrespective to whether it comes from cufflinks or cuffdiff ?
What should I do now, consider cuifflinks FPKM or cuffdiff FPKM ? I mainly want to compare samples in time series and on WT vs mutant. Any suggestions ?
Edited: MY main purpose is to find the half life of each Transcripts RNA, so I want to construct a plot of log(FPKM) vs time. Which FPKM should I use ?!
What should I do now, consider cuifflinks FPKM or cuffdiff FPKM ? I mainly want to compare samples in time series and on WT vs mutant. Any suggestions ?
Edited: MY main purpose is to find the half life of each Transcripts RNA, so I want to construct a plot of log(FPKM) vs time. Which FPKM should I use ?!
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