Hi there,
I have been using the Tuxedo suite tools , specifically I have been using bowtie, tophat,and cufflinks. Now that I have FPKM values I have a couple of questions.
1. What are the most common ways folks are using to normalize their FPKM data?
2. I am looking into differential expression of the FPKM values across my samples and time points. I have successfully run cuff compare but when I run cuffdiff I get results (Tested id XLOC_000001, locus, etc.) but my gene ids are not in the output. any suggestions people have on why that might be missing? I can always map the tested id with cuff compare results. Any suggestions people have are apprciated. Thanks
-Rich
I have been using the Tuxedo suite tools , specifically I have been using bowtie, tophat,and cufflinks. Now that I have FPKM values I have a couple of questions.
1. What are the most common ways folks are using to normalize their FPKM data?
2. I am looking into differential expression of the FPKM values across my samples and time points. I have successfully run cuff compare but when I run cuffdiff I get results (Tested id XLOC_000001, locus, etc.) but my gene ids are not in the output. any suggestions people have on why that might be missing? I can always map the tested id with cuff compare results. Any suggestions people have are apprciated. Thanks
-Rich
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