Use cufflinks or cuffdiff to get gene expression value？

[xiongdianguang]

I used tophat cufflinks and cuffdiff to analysis my mRNA sequencing data, I am confused about the gene expression value. We have 7 samples in my expreiment, I can used cufflinks to produce every gene's expression value(FPKM) in each stage , and I can also used cuffdiff to get the gene's expression value by running cuffdiff with 7 samples together. But the gene's expression value produced by cufflinks and cuffdiff is not the same, so could you give me a instruction about that. Thank you.

[HilmarBerger]

... But the gene's expression value produced by cufflinks and cuffdiff is not the same, so could you give me a instruction about that. Thank you.

I'm not the author of this package, but probably part of the difference can be explained by the fact that cuffdiff uses data from all replicates to estimate some parameters (e.g. count variance) and also might apply normalization if selected. The latest version of cuffdiff allows to export both per-sample FPKM and per-sample read counts for each gene. I would probably prefer those to the cufflinks output which is based solely on the data of individual samples.

[xiongdianguang]

Hi hilmarberher,
That i want to ask you,i am also confused about the gene's expression value produced by cufflinks and cuffdiff.there have different gene's expression value ,I don't know which one should i used to analysis further.